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barplot: Visualize taxonomy with an interactive bar plotΒΆ

Docstring:

Usage: qiime taxa barplot [OPTIONS]

  This visualizer produces an interactive barplot visualization of taxonomies.
  Interactive features include multi-level sorting, plot recoloring, sample
  relabeling, and SVG figure export.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | PresenceAbsence]
                         Feature table to visualize at various taxonomic
                         levels.                                    [required]
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomic annotations for features in the provided
                         feature table. All features in the feature table must
                         have a corresponding taxonomic annotation. Taxonomic
                         annotations that are not present in the feature table
                         will be ignored. If no taxonomy is provided, the
                         feature IDs will be used as labels.        [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple            The sample metadata.
     arguments will be
     merged)                                                        [optional]
  --p-level-delimiter TEXT
                         Attempt to parse hierarchical taxonomic information
                         from feature IDs by separating levels with this
                         character. This parameter is ignored if a taxonomy is
                         provided as input.                         [optional]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.

Examples:
  # ### example: barplot
  qiime taxa barplot \
    --i-table table.qza \
    --i-taxonomy taxonomy.qza \
    --m-metadata-file sample-metadata.tsv \
    --o-visualization taxa-bar-plots.qzv

Import:

from qiime2.plugins.taxa.visualizers import barplot

Docstring:

Visualize taxonomy with an interactive bar plot

This visualizer produces an interactive barplot visualization of
taxonomies. Interactive features include multi-level sorting, plot
recoloring, sample relabeling, and SVG figure export.

Parameters
----------
table : FeatureTable[Frequency | PresenceAbsence]
    Feature table to visualize at various taxonomic levels.
taxonomy : FeatureData[Taxonomy], optional
    Taxonomic annotations for features in the provided feature table. All
    features in the feature table must have a corresponding taxonomic
    annotation. Taxonomic annotations that are not present in the feature
    table will be ignored. If no taxonomy is provided, the feature IDs will
    be used as labels.
metadata : Metadata, optional
    The sample metadata.
level_delimiter : Str, optional
    Attempt to parse hierarchical taxonomic information from feature IDs by
    separating levels with this character. This parameter is ignored if a
    taxonomy is provided as input.

Returns
-------
visualization : Visualization