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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Composition]
                                  The feature table to be used for ANCOM
                                  computation.  [required]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata.
                                  [required]
  --m-metadata-column MetadataColumn[Categorical]
                                  Column from metadata file or artifact
                                  viewable as metadata. The categorical sample
                                  metadata column to test for differential
                                  abundance across.  [required]
  --p-transform-function [sqrt|clr|log]
                                  The method applied to transform feature
                                  values before generating volcano plots.
                                  [default: clr]
  --p-difference-function [mean_difference|f_statistic]
                                  The method applied to visualize fold
                                  difference in feature abundances across
                                  groups for volcano plots.  [optional]
  --o-visualization VISUALIZATION PATH
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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({'clr', 'log', 'sqrt'}), optional
    The method applied to transform feature values before generating
    volcano plots.
difference_function : Str % Choices({'f_statistic', 'mean_difference'}), optional
    The method applied to visualize fold difference in feature abundances
    across groups for volcano plots.

Returns
-------
visualization : Visualization