q2-emperor

qiime2

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

Generates an interactive ordination biplot where the user can visually integrate sample and feature metadata. Vectors representing the n most important features are then plotted in the emperor visualization (5 largest, by default).

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor biplot¶

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor biplot¶

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor biplot¶

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor biplot¶

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor biplot¶

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor biplot¶

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin wraps Emperor and supports interactive visualization of ordination plots.

version: 2024.10.0
website: http://biocore.github.io/emperor/build/html/index.html
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org
citations:: Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Actions¶

Name	Type	Short Description
plot	visualizer	Visualize and Interact with Principal Coordinates Analysis Plots
procrustes-plot	visualizer	Visualize and Interact with a procrustes plot
biplot	visualizer	Visualize and Interact with Principal Coordinates Analysis Biplot

emperor plot¶

Generates an interactive ordination plot where the user can visually integrate sample metadata.

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

pcoa: PCoAResults: The principal coordinates matrix to be plotted.[required]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
ignore_pcoa_features: Bool: Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the biplot method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

emperor_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'

qiime emperor plot \
  --i-pcoa pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn = 'pcoa-result.qza'
request.urlretrieve(url, fn)
pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

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

Using the qiime2 emperor plot tool:

Set "pcoa" to #: pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/pcoa-result.qza'
fn <- 'pcoa-result.qza'
request$urlretrieve(url, fn)
pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$plot(
    pcoa=pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor procrustes-plot¶

Plot two procrustes-fitted matrices

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

reference_pcoa: PCoAResults: The reference ordination matrix to be plotted.[required]
other_pcoa: PCoAResults: The "other" ordination matrix to be plotted (the one that was fitted to the reference).[required]
m2_stats: ProcrustesStatistics: The M^2 value of the procrustes analysis & its associated p value.[optional]

Parameters¶

metadata: Metadata: The sample metadata.[required]
custom_axes: List[Str]: Numeric sample metadata columns that should be included as axes in the Emperor plot.[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

procrustes_plot¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'bc-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'

wget -O 'unw-pcoa-result.qza' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'

wget -O 'sample-metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'

qiime emperor procrustes-plot \
  --i-reference-pcoa bc-pcoa-result.qza \
  --i-other-pcoa unw-pcoa-result.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization plot.qzv

from qiime2 import Artifact
from qiime2 import Metadata
from urllib import request
import qiime2.plugins.emperor.actions as emperor_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn = 'bc-pcoa-result.qza'
request.urlretrieve(url, fn)
bc_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn = 'unw-pcoa-result.qza'
request.urlretrieve(url, fn)
unw_pcoa_result = Artifact.load(fn)

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn = 'sample-metadata.tsv'
request.urlretrieve(url, fn)
sample_metadata_md = Metadata.load(fn)

plot_viz, = emperor_actions.procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)

Using the Upload Data tool:

On the first tab (Regular), press the Paste/Fetch data button at the bottom.
1. Set "Name" (first text-field) to: bc-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.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: unw-pcoa-result.qza
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.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: sample-metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 emperor procrustes-plot tool:

Set "reference_pcoa" to #: bc-pcoa-result.qza
Set "other_pcoa" to #: unw-pcoa-result.qza
For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to sample-metadata.tsv
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 emperor procrustes-plot [...] : visualization.qzv`	`plot.qzv`

library(reticulate)

Artifact <- import("qiime2")$Artifact
Metadata <- import("qiime2")$Metadata
emperor_actions <- import("qiime2.plugins.emperor.actions")
request <- import("urllib")$request

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/bc-pcoa-result.qza'
fn <- 'bc-pcoa-result.qza'
request$urlretrieve(url, fn)
bc_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/unw-pcoa-result.qza'
fn <- 'unw-pcoa-result.qza'
request$urlretrieve(url, fn)
unw_pcoa_result <- Artifact$load(fn)

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/emperor/procrustes-plot/1/sample-metadata.tsv'
fn <- 'sample-metadata.tsv'
request$urlretrieve(url, fn)
sample_metadata_md <- Metadata$load(fn)

action_results <- emperor_actions$procrustes_plot(
    reference_pcoa=bc_pcoa_result,
    other_pcoa=unw_pcoa_result,
    metadata=sample_metadata_md,
)
plot_viz <- action_results$visualization

bc-pcoa-result.qza | download | view
unw-pcoa-result.qza | download | view
sample-metadata.tsv | download
plot.qzv | download | view

emperor biplot¶

Citations¶

Vázquez-Baeza et al., 2013; Vázquez-Baeza et al., 2017

Inputs¶

biplot: PCoAResults % Properties('biplot'): The principal coordinates matrix to be plotted.[required]

Parameters¶

sample_metadata: Metadata: The sample metadata[required]
feature_metadata: Metadata: The feature metadata (useful to manipulate the arrows in the plot).[optional]
ignore_missing_samples: Bool: This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.[default: False]
invert: Bool: If specified, the point and arrow coordinates will be swapped.[default: False]
number_of_features: Int % Range(1, None): The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).[default: 5]

Outputs¶

visualization: Visualization: <no description>[required]

Links

Documentation

Source Code

Stars

Last Commit

018b885

Available Distros

2024.10: 2024.10/amplicon; 2024.10/metagenome
2024.5: 2024.5/amplicon; 2024.5/metagenome
2024.2: 2024.2/amplicon
2023.9: 2023.9/amplicon
2023.7: 2023.7/core