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group: Group samples or features by a metadata columnΒΆ

Docstring:

Usage: qiime feature-table group [OPTIONS]

  Group samples or features in a feature table using metadata to define the
  mapping of IDs to a group.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                       The table to group samples or features on.   [required]
Parameters:
  --p-axis TEXT Choices('feature', 'sample')
                       Along which axis to group. Each ID in the given axis
                       must exist in `metadata`.                    [required]
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Categorical]
                       A column defining the groups. Each unique value will
                       become a new ID for the table on the given `axis`.
                                                                    [required]
  --p-mode TEXT Choices('sum', 'mean-ceiling', 'median-ceiling')
                       How to combine samples or features within a group.
                       `sum` will sum the frequencies across all samples or
                       features within a group; `mean-ceiling` will take the
                       ceiling of the mean of these frequencies;
                       `median-ceiling` will take the ceiling of the median of
                       these frequencies.                           [required]
Outputs:
  --o-grouped-table ARTIFACT FeatureTable[Frequency]
                       A table that has been grouped along the given `axis`.
                       IDs on that axis are replaced by values in the
                       `metadata` column.                           [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.feature_table.methods import group

Docstring:

Group samples or features by a metadata column

Group samples or features in a feature table using metadata to define the
mapping of IDs to a group.

Parameters
----------
table : FeatureTable[Frequency]
    The table to group samples or features on.
axis : Str % Choices('sample', 'feature')
    Along which axis to group. Each ID in the given axis must exist in
    `metadata`.
metadata : MetadataColumn[Categorical]
    A column defining the groups. Each unique value will become a new ID
    for the table on the given `axis`.
mode : Str % Choices('median-ceiling', 'mean-ceiling', 'sum')
    How to combine samples or features within a group. `sum` will sum the
    frequencies across all samples or features within a group; `mean-
    ceiling` will take the ceiling of the mean of these frequencies;
    `median-ceiling` will take the ceiling of the median of these
    frequencies.

Returns
-------
grouped_table : FeatureTable[Frequency]
    A table that has been grouped along the given `axis`. IDs on that axis
    are replaced by values in the `metadata` column.