Fork me on GitHub

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('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.                      [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).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.

Examples:
  # ### example: group samples
  # Combine samples from the same body-site into single sample. Feature
  # frequencies will be the median across the samples being combined, rounded
  # up to the nearest whole number.
  qiime feature-table group \
    --i-table feature-table.qza \
    --m-metadata-file sample-metadata.tsv \
    --m-metadata-column body-site \
    --p-mode median-ceiling \
    --p-axis sample \
    --o-grouped-table body-site-table.qza

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.