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ancom: Apply ANCOM to identify features that differ in abundance.ΒΆ

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]
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).
  --citations          Show citations and exit.
  --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.

Returns
-------
visualization : Visualization