q2-diversity-lib

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Shannon's Entropy should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Shannon's Entropy.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

Compute Bray-Curtis dissimilarity for each sample in a feature table. Note: Frequency and relative frequency data produce different results unless overall sample sizes are identical. Please consider the impact on your results if you use Bray-Curtis with count data that has not been adjusted (normalized).

Citations¶

Sørensen, 1948

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Bray-Curtis dissimilarity[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs=1L,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs='auto',
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

diversity-lib jaccard¶

Compute Jaccard distance for each sample in a feature table. Jaccard is calculated usingpresence/absence data. Data of type FeatureTable[Frequency | Relative Frequency] is reducedto presence/absence prior to calculation.

Citations¶

Jaccard, 1908

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Jaccard distance should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Jaccard index[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs=1L,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs='auto',
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

diversity-lib unweighted-unifrac¶

Compute Unweighted Unifrac for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Unweighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

diversity-lib weighted-unifrac¶

Compute Weighted Unifrac for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Weighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

diversity-lib alpha-passthrough¶

Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples for which a selected metric should be computed.[required]

Parameters¶

metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong'): The alpha diversity metric to be computed.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for the chosen metric.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'

qiime diversity-lib alpha-passthrough \
  --i-table feature-table.qza \
  --p-metric simpson \
  --o-vector simpson-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

simpson_vector, = diversity_lib_actions.alpha_passthrough(
    table=feature_table,
    metric='simpson',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib alpha-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to simpson
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza`	`simpson-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$alpha_passthrough(
    table=feature_table,
    metric='simpson',
)
simpson_vector <- action_results$vector

feature-table.qza | download | view
simpson-vector.qza | download | view

diversity-lib beta-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]

Parameters¶

metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'): The beta diversity metric to be computed.[required]
pseudocount: Int % Range(1, None): A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics.[default: 1]
n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1L,
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'

# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

use 'pseudocount' to manually set a pseudocount for compositional metrics¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Expand the additional options section
- Set "pseudocount" to 5
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5L,
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

diversity-lib beta-phylogenetic-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Sfiligoi et al., n.d.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=TRUE,
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

variance adjustment¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Chang et al's variance adjustment may be applied to any unifrac method by
# using this passthrough function.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_unifrac \
  --p-threads auto \
  --p-variance-adjusted \
  --o-distance-matrix var-adj-weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

var_adj_weighted_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=True,
)

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_unifrac
Expand the additional options section
- Set "variance_adjusted" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`var-adj-weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=TRUE,
)
var_adj_weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
var-adj-weighted-unifrac-dm.qza | download | view

minimal generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Generalized unifrac is passed alpha=1 by default. This is roughly
# equivalent to weighted normalized unifrac, which method will be used
# instead, because it is better optimized.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# passing a float between 0 and 1 to 'alpha' gives you control over the
# importance of sample proportions.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --p-alpha 0.75 \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Expand the additional options section
- Set "alpha" to 0.75
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

diversity-lib beta-phylogenetic-meta-passthrough¶

Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Lozupone et al., 2008

Inputs¶

tables: List[FeatureTable[Frequency]]: The feature tables containing the samples over which beta diversity should be computed.[required]
phylogenies: List[Phylogeny[Rooted]]: Phylogenetic trees containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]
weights: List[Float]: The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly.[optional]
consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values'): The matrix consolidation method, which determines how the individual distance matrices are aggregated[default: 'skipping_missing_values']

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

Basic meta unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# For brevity, these examples are focused on meta-specific parameters. See
# the documentation for beta_phylogenetic_passthrough for additional
# relevant information.
wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'

# NOTE: the number of trees and tables must match.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

# NOTE: the number of trees and tables must match.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
)

For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

NOTE: the number of trees and tables must match.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

# NOTE: the number of trees and tables must match.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

meta with weights¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny.qza phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 3.0 42.0 \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny, phylogeny],
    metric='weighted_normalized_unifrac',
    weights=[3.0, 42.0],
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

The number of weights must match the number of tables/trees.

If meaningful, it is possible to pass the same phylogeny more than once.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny.qza
2. #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 3.0
  2. Add "element" set to 42.0
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny, phylogeny),
    metric='weighted_normalized_unifrac',
    weights=list(3.0, 42.0),
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

changing the consolidation method¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'

qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 0.4 0.6 \
  --p-consolidation skipping_missing_values \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
    weights=[0.4, 0.6],
    consolidation='skipping_missing_values',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
1. For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 0.4
  2. Add "element" set to 0.6
2. Leave "consolidation" as its default value of skipping_missing_values
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
    weights=list(0.4, 0.6),
    consolidation='skipping_missing_values',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

This QIIME 2 plugin computes individual metrics for community alpha and beta diversity.

version: 2024.10.0
website: https://github.com/qiime2/q2-diversity-lib
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
faith-pd	method	Faith's Phylogenetic Diversity
observed-features	method	Observed Features
pielou-evenness	method	Pielou's Evenness
shannon-entropy	method	Shannon's Entropy
bray-curtis	method	Bray-Curtis Dissimilarity
jaccard	method	Jaccard Distance
unweighted-unifrac	method	Unweighted Unifrac
weighted-unifrac	method	Weighted Unifrac
alpha-passthrough	method	Alpha Passthrough (non-phylogenetic)
beta-passthrough	method	Beta Passthrough (non-phylogenetic)
beta-phylogenetic-passthrough	method	Beta Phylogenetic Passthrough
beta-phylogenetic-meta-passthrough	method	Beta Phylogenetic Meta Passthrough

diversity-lib faith-pd¶

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Shannon's Entropy should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Shannon's Entropy.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

diversity-lib bray-curtis¶

Citations¶

Sørensen, 1948

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Bray-Curtis dissimilarity[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs=1L,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs='auto',
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

diversity-lib jaccard¶

Citations¶

Jaccard, 1908

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Jaccard distance should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Jaccard index[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs=1L,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs='auto',
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

diversity-lib unweighted-unifrac¶

Compute Unweighted Unifrac for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Unweighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

diversity-lib weighted-unifrac¶

Compute Weighted Unifrac for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Weighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

diversity-lib alpha-passthrough¶

Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples for which a selected metric should be computed.[required]

Parameters¶

metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong'): The alpha diversity metric to be computed.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for the chosen metric.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'

qiime diversity-lib alpha-passthrough \
  --i-table feature-table.qza \
  --p-metric simpson \
  --o-vector simpson-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

simpson_vector, = diversity_lib_actions.alpha_passthrough(
    table=feature_table,
    metric='simpson',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib alpha-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to simpson
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza`	`simpson-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$alpha_passthrough(
    table=feature_table,
    metric='simpson',
)
simpson_vector <- action_results$vector

feature-table.qza | download | view
simpson-vector.qza | download | view

diversity-lib beta-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]

Parameters¶

metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'): The beta diversity metric to be computed.[required]
pseudocount: Int % Range(1, None): A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics.[default: 1]
n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1L,
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'

# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

use 'pseudocount' to manually set a pseudocount for compositional metrics¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Expand the additional options section
- Set "pseudocount" to 5
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5L,
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

diversity-lib beta-phylogenetic-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Sfiligoi et al., n.d.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=TRUE,
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

variance adjustment¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Chang et al's variance adjustment may be applied to any unifrac method by
# using this passthrough function.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_unifrac \
  --p-threads auto \
  --p-variance-adjusted \
  --o-distance-matrix var-adj-weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

var_adj_weighted_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=True,
)

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_unifrac
Expand the additional options section
- Set "variance_adjusted" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`var-adj-weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=TRUE,
)
var_adj_weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
var-adj-weighted-unifrac-dm.qza | download | view

minimal generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Generalized unifrac is passed alpha=1 by default. This is roughly
# equivalent to weighted normalized unifrac, which method will be used
# instead, because it is better optimized.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# passing a float between 0 and 1 to 'alpha' gives you control over the
# importance of sample proportions.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --p-alpha 0.75 \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Expand the additional options section
- Set "alpha" to 0.75
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

diversity-lib beta-phylogenetic-meta-passthrough¶

Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Lozupone et al., 2008

Inputs¶

tables: List[FeatureTable[Frequency]]: The feature tables containing the samples over which beta diversity should be computed.[required]
phylogenies: List[Phylogeny[Rooted]]: Phylogenetic trees containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]
weights: List[Float]: The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly.[optional]
consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values'): The matrix consolidation method, which determines how the individual distance matrices are aggregated[default: 'skipping_missing_values']

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

Basic meta unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# For brevity, these examples are focused on meta-specific parameters. See
# the documentation for beta_phylogenetic_passthrough for additional
# relevant information.
wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'

# NOTE: the number of trees and tables must match.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

# NOTE: the number of trees and tables must match.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
)

For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

NOTE: the number of trees and tables must match.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

# NOTE: the number of trees and tables must match.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

meta with weights¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny.qza phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 3.0 42.0 \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny, phylogeny],
    metric='weighted_normalized_unifrac',
    weights=[3.0, 42.0],
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

The number of weights must match the number of tables/trees.

If meaningful, it is possible to pass the same phylogeny more than once.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny.qza
2. #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 3.0
  2. Add "element" set to 42.0
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny, phylogeny),
    metric='weighted_normalized_unifrac',
    weights=list(3.0, 42.0),
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

changing the consolidation method¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'

qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 0.4 0.6 \
  --p-consolidation skipping_missing_values \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
    weights=[0.4, 0.6],
    consolidation='skipping_missing_values',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
1. For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 0.4
  2. Add "element" set to 0.6
2. Leave "consolidation" as its default value of skipping_missing_values
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
    weights=list(0.4, 0.6),
    consolidation='skipping_missing_values',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

This QIIME 2 plugin computes individual metrics for community alpha and beta diversity.

version: 2024.10.0
website: https://github.com/qiime2/q2-diversity-lib
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
faith-pd	method	Faith's Phylogenetic Diversity
observed-features	method	Observed Features
pielou-evenness	method	Pielou's Evenness
shannon-entropy	method	Shannon's Entropy
bray-curtis	method	Bray-Curtis Dissimilarity
jaccard	method	Jaccard Distance
unweighted-unifrac	method	Unweighted Unifrac
weighted-unifrac	method	Weighted Unifrac
alpha-passthrough	method	Alpha Passthrough (non-phylogenetic)
beta-passthrough	method	Beta Passthrough (non-phylogenetic)
beta-phylogenetic-passthrough	method	Beta Phylogenetic Passthrough
beta-phylogenetic-meta-passthrough	method	Beta Phylogenetic Meta Passthrough

diversity-lib faith-pd¶

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Shannon's Entropy should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Shannon's Entropy.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

diversity-lib bray-curtis¶

Citations¶

Sørensen, 1948

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Bray-Curtis dissimilarity[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs=1L,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs='auto',
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

diversity-lib jaccard¶

Citations¶

Jaccard, 1908

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Jaccard distance should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Jaccard index[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs=1L,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs='auto',
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

diversity-lib unweighted-unifrac¶

Compute Unweighted Unifrac for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Unweighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

diversity-lib weighted-unifrac¶

Compute Weighted Unifrac for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Weighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

diversity-lib alpha-passthrough¶

Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples for which a selected metric should be computed.[required]

Parameters¶

metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong'): The alpha diversity metric to be computed.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for the chosen metric.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'

qiime diversity-lib alpha-passthrough \
  --i-table feature-table.qza \
  --p-metric simpson \
  --o-vector simpson-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

simpson_vector, = diversity_lib_actions.alpha_passthrough(
    table=feature_table,
    metric='simpson',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib alpha-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to simpson
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza`	`simpson-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$alpha_passthrough(
    table=feature_table,
    metric='simpson',
)
simpson_vector <- action_results$vector

feature-table.qza | download | view
simpson-vector.qza | download | view

diversity-lib beta-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]

Parameters¶

metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'): The beta diversity metric to be computed.[required]
pseudocount: Int % Range(1, None): A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics.[default: 1]
n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1L,
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'

# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

use 'pseudocount' to manually set a pseudocount for compositional metrics¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Expand the additional options section
- Set "pseudocount" to 5
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5L,
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

diversity-lib beta-phylogenetic-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Sfiligoi et al., n.d.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=TRUE,
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

variance adjustment¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Chang et al's variance adjustment may be applied to any unifrac method by
# using this passthrough function.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_unifrac \
  --p-threads auto \
  --p-variance-adjusted \
  --o-distance-matrix var-adj-weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

var_adj_weighted_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=True,
)

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_unifrac
Expand the additional options section
- Set "variance_adjusted" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`var-adj-weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=TRUE,
)
var_adj_weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
var-adj-weighted-unifrac-dm.qza | download | view

minimal generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Generalized unifrac is passed alpha=1 by default. This is roughly
# equivalent to weighted normalized unifrac, which method will be used
# instead, because it is better optimized.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# passing a float between 0 and 1 to 'alpha' gives you control over the
# importance of sample proportions.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --p-alpha 0.75 \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Expand the additional options section
- Set "alpha" to 0.75
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

diversity-lib beta-phylogenetic-meta-passthrough¶

Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Lozupone et al., 2008

Inputs¶

tables: List[FeatureTable[Frequency]]: The feature tables containing the samples over which beta diversity should be computed.[required]
phylogenies: List[Phylogeny[Rooted]]: Phylogenetic trees containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]
weights: List[Float]: The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly.[optional]
consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values'): The matrix consolidation method, which determines how the individual distance matrices are aggregated[default: 'skipping_missing_values']

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

Basic meta unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# For brevity, these examples are focused on meta-specific parameters. See
# the documentation for beta_phylogenetic_passthrough for additional
# relevant information.
wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'

# NOTE: the number of trees and tables must match.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

# NOTE: the number of trees and tables must match.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
)

For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

NOTE: the number of trees and tables must match.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

# NOTE: the number of trees and tables must match.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

meta with weights¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny.qza phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 3.0 42.0 \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny, phylogeny],
    metric='weighted_normalized_unifrac',
    weights=[3.0, 42.0],
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

The number of weights must match the number of tables/trees.

If meaningful, it is possible to pass the same phylogeny more than once.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny.qza
2. #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 3.0
  2. Add "element" set to 42.0
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny, phylogeny),
    metric='weighted_normalized_unifrac',
    weights=list(3.0, 42.0),
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

changing the consolidation method¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'

qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 0.4 0.6 \
  --p-consolidation skipping_missing_values \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
    weights=[0.4, 0.6],
    consolidation='skipping_missing_values',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
1. For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 0.4
  2. Add "element" set to 0.6
2. Leave "consolidation" as its default value of skipping_missing_values
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
    weights=list(0.4, 0.6),
    consolidation='skipping_missing_values',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

This QIIME 2 plugin computes individual metrics for community alpha and beta diversity.

version: 2024.10.0
website: https://github.com/qiime2/q2-diversity-lib
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
faith-pd	method	Faith's Phylogenetic Diversity
observed-features	method	Observed Features
pielou-evenness	method	Pielou's Evenness
shannon-entropy	method	Shannon's Entropy
bray-curtis	method	Bray-Curtis Dissimilarity
jaccard	method	Jaccard Distance
unweighted-unifrac	method	Unweighted Unifrac
weighted-unifrac	method	Weighted Unifrac
alpha-passthrough	method	Alpha Passthrough (non-phylogenetic)
beta-passthrough	method	Beta Passthrough (non-phylogenetic)
beta-phylogenetic-passthrough	method	Beta Phylogenetic Passthrough
beta-phylogenetic-meta-passthrough	method	Beta Phylogenetic Meta Passthrough

diversity-lib faith-pd¶

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Shannon's Entropy should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Shannon's Entropy.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

diversity-lib bray-curtis¶

Citations¶

Sørensen, 1948

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Bray-Curtis dissimilarity[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs=1L,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs='auto',
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

diversity-lib jaccard¶

Citations¶

Jaccard, 1908

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Jaccard distance should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Jaccard index[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs=1L,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs='auto',
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

diversity-lib unweighted-unifrac¶

Compute Unweighted Unifrac for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Unweighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

diversity-lib weighted-unifrac¶

Compute Weighted Unifrac for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Weighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

diversity-lib alpha-passthrough¶

Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples for which a selected metric should be computed.[required]

Parameters¶

metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong'): The alpha diversity metric to be computed.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for the chosen metric.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'

qiime diversity-lib alpha-passthrough \
  --i-table feature-table.qza \
  --p-metric simpson \
  --o-vector simpson-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

simpson_vector, = diversity_lib_actions.alpha_passthrough(
    table=feature_table,
    metric='simpson',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib alpha-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to simpson
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza`	`simpson-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$alpha_passthrough(
    table=feature_table,
    metric='simpson',
)
simpson_vector <- action_results$vector

feature-table.qza | download | view
simpson-vector.qza | download | view

diversity-lib beta-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]

Parameters¶

metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'): The beta diversity metric to be computed.[required]
pseudocount: Int % Range(1, None): A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics.[default: 1]
n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1L,
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'

# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

use 'pseudocount' to manually set a pseudocount for compositional metrics¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Expand the additional options section
- Set "pseudocount" to 5
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5L,
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

diversity-lib beta-phylogenetic-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Sfiligoi et al., n.d.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=TRUE,
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

variance adjustment¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Chang et al's variance adjustment may be applied to any unifrac method by
# using this passthrough function.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_unifrac \
  --p-threads auto \
  --p-variance-adjusted \
  --o-distance-matrix var-adj-weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

var_adj_weighted_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=True,
)

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_unifrac
Expand the additional options section
- Set "variance_adjusted" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`var-adj-weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=TRUE,
)
var_adj_weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
var-adj-weighted-unifrac-dm.qza | download | view

minimal generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Generalized unifrac is passed alpha=1 by default. This is roughly
# equivalent to weighted normalized unifrac, which method will be used
# instead, because it is better optimized.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# passing a float between 0 and 1 to 'alpha' gives you control over the
# importance of sample proportions.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --p-alpha 0.75 \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Expand the additional options section
- Set "alpha" to 0.75
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

diversity-lib beta-phylogenetic-meta-passthrough¶

Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Lozupone et al., 2008

Inputs¶

tables: List[FeatureTable[Frequency]]: The feature tables containing the samples over which beta diversity should be computed.[required]
phylogenies: List[Phylogeny[Rooted]]: Phylogenetic trees containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]
weights: List[Float]: The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly.[optional]
consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values'): The matrix consolidation method, which determines how the individual distance matrices are aggregated[default: 'skipping_missing_values']

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

Basic meta unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# For brevity, these examples are focused on meta-specific parameters. See
# the documentation for beta_phylogenetic_passthrough for additional
# relevant information.
wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'

# NOTE: the number of trees and tables must match.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

# NOTE: the number of trees and tables must match.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
)

For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

NOTE: the number of trees and tables must match.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

# NOTE: the number of trees and tables must match.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

meta with weights¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny.qza phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 3.0 42.0 \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny, phylogeny],
    metric='weighted_normalized_unifrac',
    weights=[3.0, 42.0],
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

The number of weights must match the number of tables/trees.

If meaningful, it is possible to pass the same phylogeny more than once.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny.qza
2. #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 3.0
  2. Add "element" set to 42.0
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny, phylogeny),
    metric='weighted_normalized_unifrac',
    weights=list(3.0, 42.0),
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

changing the consolidation method¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'

qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 0.4 0.6 \
  --p-consolidation skipping_missing_values \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
    weights=[0.4, 0.6],
    consolidation='skipping_missing_values',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
1. For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 0.4
  2. Add "element" set to 0.6
2. Leave "consolidation" as its default value of skipping_missing_values
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
    weights=list(0.4, 0.6),
    consolidation='skipping_missing_values',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

This QIIME 2 plugin computes individual metrics for community alpha and beta diversity.

version: 2024.10.0
website: https://github.com/qiime2/q2-diversity-lib
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
faith-pd	method	Faith's Phylogenetic Diversity
observed-features	method	Observed Features
pielou-evenness	method	Pielou's Evenness
shannon-entropy	method	Shannon's Entropy
bray-curtis	method	Bray-Curtis Dissimilarity
jaccard	method	Jaccard Distance
unweighted-unifrac	method	Unweighted Unifrac
weighted-unifrac	method	Weighted Unifrac
alpha-passthrough	method	Alpha Passthrough (non-phylogenetic)
beta-passthrough	method	Beta Passthrough (non-phylogenetic)
beta-phylogenetic-passthrough	method	Beta Phylogenetic Passthrough
beta-phylogenetic-meta-passthrough	method	Beta Phylogenetic Meta Passthrough

diversity-lib faith-pd¶

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Shannon's Entropy should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Shannon's Entropy.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

diversity-lib bray-curtis¶

Citations¶

Sørensen, 1948

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Bray-Curtis dissimilarity[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs=1L,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs='auto',
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

diversity-lib jaccard¶

Citations¶

Jaccard, 1908

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Jaccard distance should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Jaccard index[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs=1L,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs='auto',
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

diversity-lib unweighted-unifrac¶

Compute Unweighted Unifrac for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Unweighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

diversity-lib weighted-unifrac¶

Compute Weighted Unifrac for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Weighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

diversity-lib alpha-passthrough¶

Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples for which a selected metric should be computed.[required]

Parameters¶

metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong'): The alpha diversity metric to be computed.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for the chosen metric.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'

qiime diversity-lib alpha-passthrough \
  --i-table feature-table.qza \
  --p-metric simpson \
  --o-vector simpson-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

simpson_vector, = diversity_lib_actions.alpha_passthrough(
    table=feature_table,
    metric='simpson',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib alpha-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to simpson
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza`	`simpson-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$alpha_passthrough(
    table=feature_table,
    metric='simpson',
)
simpson_vector <- action_results$vector

feature-table.qza | download | view
simpson-vector.qza | download | view

diversity-lib beta-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]

Parameters¶

metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'): The beta diversity metric to be computed.[required]
pseudocount: Int % Range(1, None): A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics.[default: 1]
n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1L,
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'

# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

use 'pseudocount' to manually set a pseudocount for compositional metrics¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Expand the additional options section
- Set "pseudocount" to 5
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5L,
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

diversity-lib beta-phylogenetic-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Sfiligoi et al., n.d.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=TRUE,
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

variance adjustment¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Chang et al's variance adjustment may be applied to any unifrac method by
# using this passthrough function.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_unifrac \
  --p-threads auto \
  --p-variance-adjusted \
  --o-distance-matrix var-adj-weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

var_adj_weighted_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=True,
)

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_unifrac
Expand the additional options section
- Set "variance_adjusted" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`var-adj-weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=TRUE,
)
var_adj_weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
var-adj-weighted-unifrac-dm.qza | download | view

minimal generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Generalized unifrac is passed alpha=1 by default. This is roughly
# equivalent to weighted normalized unifrac, which method will be used
# instead, because it is better optimized.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# passing a float between 0 and 1 to 'alpha' gives you control over the
# importance of sample proportions.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --p-alpha 0.75 \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Expand the additional options section
- Set "alpha" to 0.75
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

diversity-lib beta-phylogenetic-meta-passthrough¶

Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Lozupone et al., 2008

Inputs¶

tables: List[FeatureTable[Frequency]]: The feature tables containing the samples over which beta diversity should be computed.[required]
phylogenies: List[Phylogeny[Rooted]]: Phylogenetic trees containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]
weights: List[Float]: The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly.[optional]
consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values'): The matrix consolidation method, which determines how the individual distance matrices are aggregated[default: 'skipping_missing_values']

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

Basic meta unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# For brevity, these examples are focused on meta-specific parameters. See
# the documentation for beta_phylogenetic_passthrough for additional
# relevant information.
wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'

# NOTE: the number of trees and tables must match.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

# NOTE: the number of trees and tables must match.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
)

For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

NOTE: the number of trees and tables must match.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

# NOTE: the number of trees and tables must match.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

meta with weights¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny.qza phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 3.0 42.0 \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny, phylogeny],
    metric='weighted_normalized_unifrac',
    weights=[3.0, 42.0],
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

The number of weights must match the number of tables/trees.

If meaningful, it is possible to pass the same phylogeny more than once.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny.qza
2. #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 3.0
  2. Add "element" set to 42.0
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny, phylogeny),
    metric='weighted_normalized_unifrac',
    weights=list(3.0, 42.0),
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

changing the consolidation method¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'

qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 0.4 0.6 \
  --p-consolidation skipping_missing_values \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
    weights=[0.4, 0.6],
    consolidation='skipping_missing_values',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
1. For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 0.4
  2. Add "element" set to 0.6
2. Leave "consolidation" as its default value of skipping_missing_values
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
    weights=list(0.4, 0.6),
    consolidation='skipping_missing_values',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

This QIIME 2 plugin computes individual metrics for community alpha and beta diversity.

version: 2024.10.0
website: https://github.com/qiime2/q2-diversity-lib
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
faith-pd	method	Faith's Phylogenetic Diversity
observed-features	method	Observed Features
pielou-evenness	method	Pielou's Evenness
shannon-entropy	method	Shannon's Entropy
bray-curtis	method	Bray-Curtis Dissimilarity
jaccard	method	Jaccard Distance
unweighted-unifrac	method	Unweighted Unifrac
weighted-unifrac	method	Weighted Unifrac
alpha-passthrough	method	Alpha Passthrough (non-phylogenetic)
beta-passthrough	method	Beta Passthrough (non-phylogenetic)
beta-phylogenetic-passthrough	method	Beta Phylogenetic Passthrough
beta-phylogenetic-meta-passthrough	method	Beta Phylogenetic Meta Passthrough

diversity-lib faith-pd¶

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Shannon's Entropy should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Shannon's Entropy.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

diversity-lib bray-curtis¶

Citations¶

Sørensen, 1948

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Bray-Curtis dissimilarity[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs=1L,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs='auto',
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

diversity-lib jaccard¶

Citations¶

Jaccard, 1908

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Jaccard distance should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Jaccard index[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs=1L,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs='auto',
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

diversity-lib unweighted-unifrac¶

Compute Unweighted Unifrac for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Unweighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

diversity-lib weighted-unifrac¶

Compute Weighted Unifrac for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Weighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

diversity-lib alpha-passthrough¶

Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples for which a selected metric should be computed.[required]

Parameters¶

metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong'): The alpha diversity metric to be computed.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for the chosen metric.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'

qiime diversity-lib alpha-passthrough \
  --i-table feature-table.qza \
  --p-metric simpson \
  --o-vector simpson-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

simpson_vector, = diversity_lib_actions.alpha_passthrough(
    table=feature_table,
    metric='simpson',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib alpha-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to simpson
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza`	`simpson-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$alpha_passthrough(
    table=feature_table,
    metric='simpson',
)
simpson_vector <- action_results$vector

feature-table.qza | download | view
simpson-vector.qza | download | view

diversity-lib beta-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]

Parameters¶

metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'): The beta diversity metric to be computed.[required]
pseudocount: Int % Range(1, None): A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics.[default: 1]
n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1L,
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'

# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

use 'pseudocount' to manually set a pseudocount for compositional metrics¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Expand the additional options section
- Set "pseudocount" to 5
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5L,
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

diversity-lib beta-phylogenetic-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Sfiligoi et al., n.d.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=TRUE,
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

variance adjustment¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Chang et al's variance adjustment may be applied to any unifrac method by
# using this passthrough function.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_unifrac \
  --p-threads auto \
  --p-variance-adjusted \
  --o-distance-matrix var-adj-weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

var_adj_weighted_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=True,
)

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_unifrac
Expand the additional options section
- Set "variance_adjusted" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`var-adj-weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=TRUE,
)
var_adj_weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
var-adj-weighted-unifrac-dm.qza | download | view

minimal generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Generalized unifrac is passed alpha=1 by default. This is roughly
# equivalent to weighted normalized unifrac, which method will be used
# instead, because it is better optimized.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# passing a float between 0 and 1 to 'alpha' gives you control over the
# importance of sample proportions.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --p-alpha 0.75 \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Expand the additional options section
- Set "alpha" to 0.75
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

diversity-lib beta-phylogenetic-meta-passthrough¶

Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Lozupone et al., 2008

Inputs¶

tables: List[FeatureTable[Frequency]]: The feature tables containing the samples over which beta diversity should be computed.[required]
phylogenies: List[Phylogeny[Rooted]]: Phylogenetic trees containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]
weights: List[Float]: The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly.[optional]
consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values'): The matrix consolidation method, which determines how the individual distance matrices are aggregated[default: 'skipping_missing_values']

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

Basic meta unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# For brevity, these examples are focused on meta-specific parameters. See
# the documentation for beta_phylogenetic_passthrough for additional
# relevant information.
wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'

# NOTE: the number of trees and tables must match.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

# NOTE: the number of trees and tables must match.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
)

For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

NOTE: the number of trees and tables must match.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

# NOTE: the number of trees and tables must match.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

meta with weights¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny.qza phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 3.0 42.0 \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny, phylogeny],
    metric='weighted_normalized_unifrac',
    weights=[3.0, 42.0],
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

The number of weights must match the number of tables/trees.

If meaningful, it is possible to pass the same phylogeny more than once.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny.qza
2. #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 3.0
  2. Add "element" set to 42.0
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny, phylogeny),
    metric='weighted_normalized_unifrac',
    weights=list(3.0, 42.0),
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

changing the consolidation method¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'

qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 0.4 0.6 \
  --p-consolidation skipping_missing_values \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
    weights=[0.4, 0.6],
    consolidation='skipping_missing_values',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
1. For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 0.4
  2. Add "element" set to 0.6
2. Leave "consolidation" as its default value of skipping_missing_values
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
    weights=list(0.4, 0.6),
    consolidation='skipping_missing_values',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

This QIIME 2 plugin computes individual metrics for community alpha and beta diversity.

version: 2024.10.0
website: https://github.com/qiime2/q2-diversity-lib
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
faith-pd	method	Faith's Phylogenetic Diversity
observed-features	method	Observed Features
pielou-evenness	method	Pielou's Evenness
shannon-entropy	method	Shannon's Entropy
bray-curtis	method	Bray-Curtis Dissimilarity
jaccard	method	Jaccard Distance
unweighted-unifrac	method	Unweighted Unifrac
weighted-unifrac	method	Weighted Unifrac
alpha-passthrough	method	Alpha Passthrough (non-phylogenetic)
beta-passthrough	method	Beta Passthrough (non-phylogenetic)
beta-phylogenetic-passthrough	method	Beta Phylogenetic Passthrough
beta-phylogenetic-meta-passthrough	method	Beta Phylogenetic Meta Passthrough

diversity-lib faith-pd¶

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Shannon's Entropy should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Shannon's Entropy.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'

qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

shannon_vector, = diversity_lib_actions.shannon_entropy(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib shannon-entropy tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib shannon-entropy [...] : vector.qza`	`shannon-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/shannon-entropy/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$shannon_entropy(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
shannon_vector <- action_results$vector

feature-table.qza | download | view
shannon-vector.qza | download | view

diversity-lib bray-curtis¶

Citations¶

Sørensen, 1948

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Bray-Curtis dissimilarity[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs=1L,
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'

qiime diversity-lib bray-curtis \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix bray-curtis-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

bray_curtis_dm, = diversity_lib_actions.bray_curtis(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib bray-curtis tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza`	`bray-curtis-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/bray-curtis/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$bray_curtis(
    table=feature_table,
    n_jobs='auto',
)
bray_curtis_dm <- action_results$distance_matrix

feature-table.qza | download | view
bray-curtis-dm.qza | download | view

diversity-lib jaccard¶

Citations¶

Jaccard, 1908

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Jaccard distance should be computed.[required]

Parameters¶

n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Jaccard index[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs 1 \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs=1L,
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'

qiime diversity-lib jaccard \
  --i-table feature-table.qza \
  --p-n-jobs auto \
  --o-distance-matrix jaccard-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

jaccard_dm, = diversity_lib_actions.jaccard(
    table=feature_table,
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib jaccard tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`	`jaccard-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/jaccard/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$jaccard(
    table=feature_table,
    n_jobs='auto',
)
jaccard_dm <- action_results$distance_matrix

feature-table.qza | download | view
jaccard-dm.qza | download | view

diversity-lib unweighted-unifrac¶

Compute Unweighted Unifrac for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Unweighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'

qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib unweighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix unweighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
unweighted_unifrac_dm, = diversity_lib_actions.unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib unweighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib unweighted-unifrac [...] : distance_matrix.qza`	`unweighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/unweighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$unweighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
unweighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
unweighted-unifrac-dm.qza | download | view

diversity-lib weighted-unifrac¶

Compute Weighted Unifrac for each sample in a feature table

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Weighted Unifrac should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: Distance matrix for Unweighted Unifrac.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'

qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_unifrac_dm, = diversity_lib_actions.weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib weighted-unifrac tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`	`weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/weighted-unifrac/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$weighted_unifrac(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    bypass_tips=TRUE,
)
weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-unifrac-dm.qza | download | view

diversity-lib alpha-passthrough¶

Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples for which a selected metric should be computed.[required]

Parameters¶

metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong'): The alpha diversity metric to be computed.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for the chosen metric.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'

qiime diversity-lib alpha-passthrough \
  --i-table feature-table.qza \
  --p-metric simpson \
  --o-vector simpson-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

simpson_vector, = diversity_lib_actions.alpha_passthrough(
    table=feature_table,
    metric='simpson',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib alpha-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to simpson
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib alpha-passthrough [...] : vector.qza`	`simpson-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/alpha-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$alpha_passthrough(
    table=feature_table,
    metric='simpson',
)
simpson_vector <- action_results$vector

feature-table.qza | download | view
simpson-vector.qza | download | view

diversity-lib beta-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]

Parameters¶

metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'): The beta diversity metric to be computed.[required]
pseudocount: Int % Range(1, None): A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics.[default: 1]
n_jobs: Threads: The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.[default: 1]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

euclidean_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to euclidean
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`euclidean-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='euclidean',
    n_jobs=1L,
)
euclidean_dm <- action_results$distance_matrix

feature-table.qza | download | view
euclidean-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'

# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

# A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

use 'pseudocount' to manually set a pseudocount for compositional metrics¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'

qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

aitchison_dm, = diversity_lib_actions.beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-passthrough tool:

Set "table" to #: feature-table.qza
Set "metric" to aitchison
Expand the additional options section
- Set "pseudocount" to 5
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-passthrough [...] : distance_matrix.qza`	`aitchison-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_passthrough(
    table=feature_table,
    metric='aitchison',
    n_jobs='auto',
    pseudocount=5L,
)
aitchison_dm <- action_results$distance_matrix

feature-table.qza | download | view
aitchison-dm.qza | download | view

diversity-lib beta-phylogenetic-passthrough¶

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Sfiligoi et al., n.d.

Inputs¶

table: FeatureTable[Frequency]: The feature table containing the samples over which beta diversity should be computed.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

run on one core (by default)¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

to run on n cores, replace 1 here with your preferred integer¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1,
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads=1L,
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use 'auto' to run on all of host system's available CPU cores¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/3/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    threads='auto',
    metric='weighted_normalized_unifrac',
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

use bypass_tips to trade specificity for reduced compute time¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'

# bypass_tips can be used with any threads setting, but auto may be a good
# choice if you're trimming run time.
qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-normalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
weighted_normalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- Set "bypass_tips" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`weighted-normalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/4/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_normalized_unifrac',
    threads='auto',
    bypass_tips=TRUE,
)
weighted_normalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
weighted-normalized-unifrac-dm.qza | download | view

variance adjustment¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Chang et al's variance adjustment may be applied to any unifrac method by
# using this passthrough function.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric weighted_unifrac \
  --p-threads auto \
  --p-variance-adjusted \
  --o-distance-matrix var-adj-weighted-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

var_adj_weighted_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=True,
)

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to weighted_unifrac
Expand the additional options section
- Set "variance_adjusted" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`var-adj-weighted-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/5/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='weighted_unifrac',
    threads='auto',
    variance_adjusted=TRUE,
)
var_adj_weighted_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
var-adj-weighted-unifrac-dm.qza | download | view

minimal generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# Generalized unifrac is passed alpha=1 by default. This is roughly
# equivalent to weighted normalized unifrac, which method will be used
# instead, because it is better optimized.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/6/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

generalized unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# passing a float between 0 and 1 to 'alpha' gives you control over the
# importance of sample proportions.
wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'

qiime diversity-lib beta-phylogenetic-passthrough \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-metric generalized_unifrac \
  --p-alpha 0.75 \
  --o-distance-matrix generalized-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

generalized_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Set "metric" to generalized_unifrac
Expand the additional options section
- Set "alpha" to 0.75
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza`	`generalized-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-passthrough/7/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_passthrough(
    table=feature_table,
    phylogeny=phylogeny,
    metric='generalized_unifrac',
    alpha=0.75,
)
generalized_unifrac_dm <- action_results$distance_matrix

feature-table.qza | download | view
phylogeny.qza | download | view
generalized-unifrac-dm.qza | download | view

diversity-lib beta-phylogenetic-meta-passthrough¶

Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Citations¶

Lozupone & Knight, 2005; Lozupone et al., 2007; Hamady et al., 2010; Lozupone et al., 2011; McDonald et al., 2018; Chang et al., 2011; Chen et al., 2012; Lozupone et al., 2008

Inputs¶

tables: List[FeatureTable[Frequency]]: The feature tables containing the samples over which beta diversity should be computed.[required]
phylogenies: List[Phylogeny[Rooted]]: Phylogenetic trees containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'): The beta diversity metric to be computed.[required]
threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]
variance_adjusted: Bool: Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.[default: False]
alpha: Float % Range(0, 1, inclusive_end=True): This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.[optional]
bypass_tips: Bool: In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs[default: False]
weights: List[Float]: The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly.[optional]
consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values'): The matrix consolidation method, which determines how the individual distance matrices are aggregated[default: 'skipping_missing_values']

Outputs¶

distance_matrix: DistanceMatrix: The resulting distance matrix.[required]

Examples¶

Basic meta unifrac¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

# For brevity, these examples are focused on meta-specific parameters. See
# the documentation for beta_phylogenetic_passthrough for additional
# relevant information.
wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'

# NOTE: the number of trees and tables must match.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

# NOTE: the number of trees and tables must match.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
)

For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

NOTE: the number of trees and tables must match.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

# For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/1/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

# NOTE: the number of trees and tables must match.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

meta with weights¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny.qza phylogeny.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 3.0 42.0 \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny, phylogeny],
    metric='weighted_normalized_unifrac',
    weights=[3.0, 42.0],
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

The number of weights must match the number of tables/trees.

If meaningful, it is possible to pass the same phylogeny more than once.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny.qza
2. #: phylogeny.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
- For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 3.0
  2. Add "element" set to 42.0
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/2/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

# The number of weights must match the number of tables/trees.
# If meaningful, it is possible to pass the same phylogeny more than once.
action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny, phylogeny),
    metric='weighted_normalized_unifrac',
    weights=list(3.0, 42.0),
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

changing the consolidation method¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'

wget -O 'feature-table2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'

wget -O 'phylogeny1.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'

wget -O 'phylogeny2.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'

qiime diversity-lib beta-phylogenetic-meta-passthrough \
  --i-tables feature-table1.qza feature-table2.qza \
  --i-phylogenies phylogeny1.qza phylogeny2.qza \
  --p-metric weighted_normalized_unifrac \
  --p-weights 0.4 0.6 \
  --p-consolidation skipping_missing_values \
  --o-distance-matrix ft1-ft2-w-norm-unifrac-dm.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn = 'feature-table1.qza'
request.urlretrieve(url, fn)
feature_table1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn = 'feature-table2.qza'
request.urlretrieve(url, fn)
feature_table2 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn = 'phylogeny1.qza'
request.urlretrieve(url, fn)
phylogeny1 = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn = 'phylogeny2.qza'
request.urlretrieve(url, fn)
phylogeny2 = Artifact.load(fn)

ft1_ft2_w_norm_unifrac_dm, = diversity_lib_actions.beta_phylogenetic_meta_passthrough(
    tables=[feature_table1, feature_table2],
    phylogenies=[phylogeny1, phylogeny2],
    metric='weighted_normalized_unifrac',
    weights=[0.4, 0.6],
    consolidation='skipping_missing_values',
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny1.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny2.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib beta-phylogenetic-meta-passthrough tool:

For "tables", use ctrl-(or command)-click to select the following inputs:
1. #: feature-table1.qza
2. #: feature-table2.qza
For "phylogenies", use ctrl-(or command)-click to select the following inputs:
1. #: phylogeny1.qza
2. #: phylogeny2.qza
Set "metric" to weighted_normalized_unifrac
Expand the additional options section
1. For "weights", use the + weights button to add the corresponding values:
  1. Add "element" set to 0.4
  2. Add "element" set to 0.6
2. Leave "consolidation" as its default value of skipping_missing_values
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza`	`ft1-ft2-w-norm-unifrac-dm.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table1.qza'
fn <- 'feature-table1.qza'
request$urlretrieve(url, fn)
feature_table1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/feature-table2.qza'
fn <- 'feature-table2.qza'
request$urlretrieve(url, fn)
feature_table2 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny1.qza'
fn <- 'phylogeny1.qza'
request$urlretrieve(url, fn)
phylogeny1 <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/beta-phylogenetic-meta-passthrough/3/phylogeny2.qza'
fn <- 'phylogeny2.qza'
request$urlretrieve(url, fn)
phylogeny2 <- Artifact$load(fn)

action_results <- diversity_lib_actions$beta_phylogenetic_meta_passthrough(
    tables=list(feature_table1, feature_table2),
    phylogenies=list(phylogeny1, phylogeny2),
    metric='weighted_normalized_unifrac',
    weights=list(0.4, 0.6),
    consolidation='skipping_missing_values',
)
ft1_ft2_w_norm_unifrac_dm <- action_results$distance_matrix

feature-table1.qza | download | view
feature-table2.qza | download | view
phylogeny1.qza | download | view
phylogeny2.qza | download | view
ft1-ft2-w-norm-unifrac-dm.qza | download | view

This QIIME 2 plugin computes individual metrics for community alpha and beta diversity.

version: 2024.10.0
website: https://github.com/qiime2/q2-diversity-lib
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
faith-pd	method	Faith's Phylogenetic Diversity
observed-features	method	Observed Features
pielou-evenness	method	Pielou's Evenness
shannon-entropy	method	Shannon's Entropy
bray-curtis	method	Bray-Curtis Dissimilarity
jaccard	method	Jaccard Distance
unweighted-unifrac	method	Unweighted Unifrac
weighted-unifrac	method	Weighted Unifrac
alpha-passthrough	method	Alpha Passthrough (non-phylogenetic)
beta-passthrough	method	Beta Passthrough (non-phylogenetic)
beta-phylogenetic-passthrough	method	Beta Phylogenetic Passthrough
beta-phylogenetic-meta-passthrough	method	Beta Phylogenetic Meta Passthrough

diversity-lib faith-pd¶

Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.[required]
phylogeny: Phylogeny[Rooted]: Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.[required]

Parameters¶

threads: Threads: The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.[default: 1]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Faith's Phylogenetic Diversity.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'

wget -O 'phylogeny.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'

qiime diversity-lib faith-pd \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-vector faith-pd-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn = 'phylogeny.qza'
request.urlretrieve(url, fn)
phylogeny = Artifact.load(fn)

faith_pd_vector, = diversity_lib_actions.faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: phylogeny.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib faith-pd tool:

Set "table" to #: feature-table.qza
Set "phylogeny" to #: phylogeny.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib faith-pd [...] : vector.qza`	`faith-pd-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/faith-pd/1/phylogeny.qza'
fn <- 'phylogeny.qza'
request$urlretrieve(url, fn)
phylogeny <- Artifact$load(fn)

action_results <- diversity_lib_actions$faith_pd(
    table=feature_table,
    phylogeny=phylogeny,
)
faith_pd_vector <- action_results$vector

feature-table.qza | download | view
phylogeny.qza | download | view
faith-pd-vector.qza | download | view

diversity-lib observed-features¶

Compute the number of observed features for each sample in a feature table

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]: The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.[required]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample counts of observed features.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'

qiime diversity-lib observed-features \
  --i-table feature-table.qza \
  --o-vector obs-feat-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

obs_feat_vector, = diversity_lib_actions.observed_features(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib observed-features tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib observed-features [...] : vector.qza`	`obs-feat-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/observed-features/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$observed_features(
    table=feature_table,
)
obs_feat_vector <- action_results$vector

feature-table.qza | download | view
obs-feat-vector.qza | download | view

diversity-lib pielou-evenness¶

Compute Pielou's Evenness for each sample in a feature table

Citations¶

Inputs¶

table: FeatureTable[Frequency | RelativeFrequency]: The feature table containing the samples for which Pielou's evenness should be computed.[required]

Parameters¶

drop_undefined_samples: Bool: Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector.[default: False]

Outputs¶

vector: SampleData[AlphaDiversity]: Vector containing per-sample values for Pielou's Evenness.[required]

Examples¶

basic¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/1/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

dropping undefined samples¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'feature-table.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'

qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza

from qiime2 import Artifact
from urllib import request
import qiime2.plugins.diversity_lib.actions as diversity_lib_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn = 'feature-table.qza'
request.urlretrieve(url, fn)
feature_table = Artifact.load(fn)

pielou_vector, = diversity_lib_actions.pielou_evenness(
    table=feature_table,
    drop_undefined_samples=True,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: feature-table.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 diversity-lib pielou-evenness tool:

Set "table" to #: feature-table.qza
Expand the additional options section
- Set "drop_undefined_samples" to Yes
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 diversity-lib pielou-evenness [...] : vector.qza`	`pielou-vector.qza`

library(reticulate)

Artifact <- import("qiime2")$Artifact
diversity_lib_actions <- import("qiime2.plugins.diversity_lib.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/diversity-lib/pielou-evenness/2/feature-table.qza'
fn <- 'feature-table.qza'
request$urlretrieve(url, fn)
feature_table <- Artifact$load(fn)

action_results <- diversity_lib_actions$pielou_evenness(
    table=feature_table,
    drop_undefined_samples=TRUE,
)
pielou_vector <- action_results$vector

feature-table.qza | download | view
pielou-vector.qza | download | view

diversity-lib shannon-entropy¶

Compute Shannon's Entropy for each sample in a feature table

Citations¶