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 [log|sqrt|clr]
The method applied to transform feature
values before generating volcano plots.
[default: clr]
--p-difference-function [f_statistic|mean_difference]
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
