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barplot: Visualize taxonomy with an interactive bar plot¶
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