q2-vizard

qiime2

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Basic lineplot for visualizing two numeric Metadata measures with optional grouping. All numeric columns present in the Metadata will be available as drop-down options on the Y-axis, but the chosen x_measure remains fixed.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

This QIIME 2 plugin is the first choice of wizard lizards for generalized microbiome data visualization!

version: 0.0.1.dev0
website: https://github.com/qiime2/q2-vizard
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
heatmap	visualizer	Heatmap
scatterplot-2d	visualizer	2D Scatterplot
lineplot	visualizer	Lineplot
boxplot	visualizer	Boxplot

vizard heatmap¶

Basic heatmap for visualizing three Metadata measures.

Parameters¶

metadata: Metadata: Any metadata-like input that contains at least three measures for visualizing, one of which must be numeric.[required]
x_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric or categorical measure from the input Metadata that should be plotted on the y-axis.[required]
gradient_measure: Str: Numeric measure from the input Metadata that should be used to represent the color gradient in the heatmap.[required]
title: Str: The title of the heatmap.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

heatmap¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/heatmap/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

heatmap_viz, = vizard_actions.heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)

Using the Upload Data tool:

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

Using the qiime2 vizard heatmap tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Set "gradient_measure" to a
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard heatmap [...] : visualization.qzv`	`heatmap.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$heatmap(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    gradient_measure='a',
)
heatmap_viz <- action_results$visualization

metadata.tsv | download
heatmap.qzv | download | view

vizard scatterplot-2d¶

Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[optional]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[optional]
color_by: Str: Categorical measure from the input Metadata that should be used for color-coding the scatterplot.[optional]
title: Str: The title of the scatterplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

scatterplot_defaults¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=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: metadata.tsv
2. In the larger text-area, copy-and-paste: https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv
3. ("Type", "Genome", and "Settings" can be ignored)
Press the Start button at the bottom.

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to 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 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/1/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

scatterplot_all_measures¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'

qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

scatterplot_viz, = vizard_actions.scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)

Using the Upload Data tool:

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

Using the qiime2 vizard scatterplot-2d tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Expand the additional options section
1. Set "x_measure" to x
2. Set "y_measure" to y
3. Set "color_by" to group
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard scatterplot-2d [...] : visualization.qzv`	`scatterplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/scatterplot-2d/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$scatterplot_2d(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    color_by='group',
)
scatterplot_viz <- action_results$visualization

metadata.tsv | download
scatterplot.qzv | download | view

vizard lineplot¶

Parameters¶

metadata: Metadata: Any metadata-like input with at least two numeric measures for visualizing.[required]
x_measure: Str: Numeric measure from the input Metadata that should be plotted on the x-axis.[required]
y_measure: Str: Numeric measure from the input Metadata that should be plotted on the y-axis.[required]
replicate_method: Str % Choices('none', 'median', 'mean'): The method for averaging replicates if present in the chosen x_measure. Available methods are median and mean.[default: 'none']
group_by: Str: Categorical measure from the input Metadata that should be used for grouping the lineplot.[optional]
title: Str: The title of the lineplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Examples¶

lineplot_median_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

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

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/1/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "group_by" to group
3. Set "title" to Lineplot with median replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

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

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='median',
    title='Lineplot with median replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-group-by group \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "group_by" to group
3. Set "title" to Lineplot with mean replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/2/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    group_by='group',
    replicate_method='mean',
    title='Lineplot with mean replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_median_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method median \
  --p-title 'Lineplot with median replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to median
2. Set "title" to Lineplot with median replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/3/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='median',
    title='Lineplot with median replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_mean_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-replicate-method mean \
  --p-title 'Lineplot with mean replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to x
Set "y_measure" to y
Expand the additional options section
1. Set "replicate_method" to mean
2. Set "title" to Lineplot with mean replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/4/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='x',
    y_measure='y',
    replicate_method='mean',
    title='Lineplot with mean replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_with_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure a \
  --p-y-measure y \
  --p-group-by group \
  --p-title 'Lineplot with no replicate method, grouped by `group`.' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to a
Set "y_measure" to y
Expand the additional options section
1. Set "group_by" to group
2. Set "title" to Lineplot with no replicate method, grouped by `group`.
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/5/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='a',
    y_measure='y',
    group_by='group',
    title='Lineplot with no replicate method, grouped by `group`.',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

lineplot_no_replicates_no_grouping¶

[Command Line]

[Python API]

[Galaxy]

[R API]

[View Source]

wget -O 'metadata.tsv' \
  'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'

qiime vizard lineplot \
  --m-metadata-file metadata.tsv \
  --p-x-measure b \
  --p-y-measure y \
  --p-title 'Lineplot with no replicate method (no grouping).' \
  --o-visualization lineplot.qzv

from qiime2 import Metadata
from urllib import request
import qiime2.plugins.vizard.actions as vizard_actions

url = 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn = 'metadata.tsv'
request.urlretrieve(url, fn)
metadata_md = Metadata.load(fn)

lineplot_viz, = vizard_actions.lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)

Using the Upload Data tool:

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

Using the qiime2 vizard lineplot tool:

For "metadata":
- Perform the following steps.
  1. Leave as Metadata from TSV
  2. Set "Metadata Source" to metadata.tsv
Set "x_measure" to b
Set "y_measure" to y
Expand the additional options section
- Set "title" to Lineplot with no replicate method (no grouping).
Press the Execute button.

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

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

History Name	"Name" to set (be sure to press [Save])
`#: qiime2 vizard lineplot [...] : visualization.qzv`	`lineplot.qzv`

library(reticulate)

Metadata <- import("qiime2")$Metadata
request <- import("urllib")$request
vizard_actions <- import("qiime2.plugins.vizard.actions")

url <- 'https://amplicon-docs.qiime2.org/en/latest/data/examples/vizard/lineplot/6/metadata.tsv'
fn <- 'metadata.tsv'
request$urlretrieve(url, fn)
metadata_md <- Metadata$load(fn)

action_results <- vizard_actions$lineplot(
    metadata=metadata_md,
    x_measure='b',
    y_measure='y',
    title='Lineplot with no replicate method (no grouping).',
)
lineplot_viz <- action_results$visualization

metadata.tsv | download
lineplot.qzv | download | view

vizard boxplot¶

Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range.

Parameters¶

metadata: Metadata: Any metadata-like input with at least one numeric measure and one categorical measure for visualizing.[required]
distribution_measure: Str: The numeric measure that will be used to create each box plot distribution.[required]
group_by: Str: The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box.[optional]
whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax'): The range that will be used for calculating the whisker lengths for each box. Options are tukeys_iqr (1.5 IQR clamped to the data extent), percentile (91th/9th percentile), or minmax. Any data points that fall outside of the chosen range will be represented as outliers that are plotted as circular points, unless the suppressOutliers checkbox has been enabled on the rendered visualization.[default: 'percentile']
box_orientation: Str % Choices('horizontal', 'vertical'): The visual orientataion of the boxes (either horizontal or vertical).[default: 'horizontal']
title: Str: The title of the boxplot.[optional]

Outputs¶

visualization: Visualization: <no description>[required]

Links

Documentation

Source Code

Stars

Last Commit

a641e5c

Available Distros

2024.10: 2024.10/amplicon; 2024.10/metagenome; 2024.10/pathogenome