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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  The table to group samples or features on.
                                  [required]
  --p-axis [feature|sample]       Along which axis to group. Each ID in the
                                  given axis must exist in `metadata`.
                                  [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. A column defining the
                                  groups. Each unique value will become a new
                                  ID for the table on the given `axis`.
                                  [required]
  --p-mode [sum|median-ceiling|mean-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]
  --o-grouped-table ARTIFACT PATH 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 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.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({'feature', 'sample'})
    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({'mean-ceiling', 'median-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.