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

Citations
  • Siddhartha Mandal, Will Van Treuren, Richard A White, Merete Eggesbø, Rob Knight, and Shyamal D Peddada. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microbial ecology in health and disease, 26(1):27663, 2015. URL: https://pubmed.ncbi.nlm.nih.gov/26028277/, doi:10.3402/mehd.v26.27663.

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.
  --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