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filter-distance-matrix: Filter samples from a distance matrix.ΒΆ

Docstring:

Usage: qiime diversity filter-distance-matrix [OPTIONS]

  Filter samples from a distance matrix, retaining only the samples matching
  search criteria specified by `metadata` and `where` parameters (or
  retaining only the samples not matching that criteria, if `exclude_ids` is
  True). See the filtering tutorial on https://docs.qiime2.org for
  additional details.

Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix     Distance matrix to filter by sample.         [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple          Sample metadata used with `where` parameter when
     arguments will    selecting samples to retain, or with `exclude-ids` when
     be merged)        selecting samples to discard.                [required]
  --p-where TEXT       SQLite WHERE clause specifying sample metadata
                       criteria that must be met to be included in the
                       filtered distance matrix. If not provided, all samples
                       in `metadata` that are also in the input distance
                       matrix will be retained.                     [optional]
  --p-exclude-ids / --p-no-exclude-ids
                       If `True`, the samples selected by `metadata` or
                       `where` parameters will be excluded from the filtered
                       distance matrix instead of being retained.
                                                              [default: False]
Outputs:
  --o-filtered-distance-matrix ARTIFACT
    DistanceMatrix     Distance matrix filtered to include samples matching
                       search criteria                              [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.diversity.methods import filter_distance_matrix

Docstring:

Filter samples from a distance matrix.

Filter samples from a distance matrix, retaining only the samples matching
search criteria specified by `metadata` and `where` parameters (or
retaining only the samples not matching that criteria, if `exclude_ids` is
True). See the filtering tutorial on https://docs.qiime2.org for additional
details.

Parameters
----------
distance_matrix : DistanceMatrix
    Distance matrix to filter by sample.
metadata : Metadata
    Sample metadata used with `where` parameter when selecting samples to
    retain, or with `exclude_ids` when selecting samples to discard.
where : Str, optional
    SQLite WHERE clause specifying sample metadata criteria that must be
    met to be included in the filtered distance matrix. If not provided,
    all samples in `metadata` that are also in the input distance matrix
    will be retained.
exclude_ids : Bool, optional
    If `True`, the samples selected by `metadata` or `where` parameters
    will be excluded from the filtered distance matrix instead of being
    retained.

Returns
-------
filtered_distance_matrix : DistanceMatrix
    Distance matrix filtered to include samples matching search criteria