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ancom: Apply ANCOM to identify features that differ in abundance.¶
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Docstring:
Usage: qiime composition ancom [OPTIONS]
Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
that are differentially abundant across groups.
Inputs:
--i-table ARTIFACT FeatureTable[Composition]
The feature table to be used for ANCOM computation.
[required]
Parameters:
--m-metadata-file METADATA
--m-metadata-column COLUMN MetadataColumn[Categorical]
The categorical sample metadata column to test for
differential abundance across. [required]
--p-transform-function TEXT Choices('sqrt', 'log', 'clr')
The method applied to transform feature values
before generating volcano plots. [default: 'clr']
--p-difference-function TEXT Choices('mean_difference', 'f_statistic')
The method applied to visualize fold difference in
feature abundances across groups for volcano plots.
[optional]
--p-filter-missing / --p-no-filter-missing
If True, samples with missing metadata values will
be filtered from the table prior to analysis. If
False, an error will be raised if there are any
missing metadata values. [default: False]
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.
Import:
from qiime2.plugins.composition.visualizers import ancom
Docstring:
Apply ANCOM to identify features that differ in abundance.
Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
that are differentially abundant across groups.
Parameters
----------
table : FeatureTable[Composition]
The feature table to be used for ANCOM computation.
metadata : MetadataColumn[Categorical]
The categorical sample metadata column to test for differential
abundance across.
transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
The method applied to transform feature values before generating
volcano plots.
difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
The method applied to visualize fold difference in feature abundances
across groups for volcano plots.
filter_missing : Bool, optional
If True, samples with missing metadata values will be filtered from the
table prior to analysis. If False, an error will be raised if there are
any missing metadata values.
Returns
-------
visualization : Visualization