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beta-correlation: Beta diversity correlationΒΆ

Docstring:

Usage: qiime diversity beta-correlation [OPTIONS]

  Create a distance matrix from a numeric metadata column and apply a two-
  sided Mantel test to identify correlation between two distance matrices.
  Actions used internally: `distance-matrix` from q2-metadata and `mantel`
  from q2-diversity.

Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix     Matrix of distances between pairs of samples.
                                                                    [required]
Parameters:
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Numeric]
                       Numeric metadata column from which to compute pairwise
                       Euclidean distances                          [required]
  --p-method TEXT Choices('spearman', 'pearson')
                       The correlation test to be applied in the Mantel test.
                                                         [default: 'spearman']
  --p-permutations INTEGER
    Range(0, None)     The number of permutations to be run when computing
                       p-values. Supplying a value of zero will disable
                       permutation testing and p-values will not be calculated
                       (this results in *much* quicker execution time if
                       p-values are not desired).               [default: 999]
  --p-intersect-ids / --p-no-intersect-ids
                       If supplied, IDs that are not found in both distance
                       matrices will be discarded before applying the Mantel
                       test. Default behavior is to error on any mismatched
                       IDs.                                   [default: False]
  --p-label1 TEXT      Label for `distance-matrix` in the output
                       visualization.                    [default: 'Metadata']
  --p-label2 TEXT      Label for `metadata-distance-matrix` in the output
                       visualization.             [default: 'Distance Matrix']
Outputs:
  --o-metadata-distance-matrix ARTIFACT
    DistanceMatrix     The Distance Matrix produced from the metadata column
                       and used in the mantel test                  [required]
  --o-mantel-scatter-visualization VISUALIZATION
                       Scatter plot rendering of the manteltest results
                                                                    [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.pipelines import beta_correlation

Docstring:

Beta diversity correlation

Create a distance matrix from a numeric metadata column and apply a two-
sided Mantel test to identify correlation between two distance matrices.
Actions used internally: `distance-matrix` from q2-metadata and `mantel`
from q2-diversity.

Parameters
----------
metadata : MetadataColumn[Numeric]
    Numeric metadata column from which to compute pairwise Euclidean
    distances
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
method : Str % Choices('spearman', 'pearson'), optional
    The correlation test to be applied in the Mantel test.
permutations : Int % Range(0, None), optional
    The number of permutations to be run when computing p-values. Supplying
    a value of zero will disable permutation testing and p-values will not
    be calculated (this results in *much* quicker execution time if
    p-values are not desired).
intersect_ids : Bool, optional
    If supplied, IDs that are not found in both distance matrices will be
    discarded before applying the Mantel test. Default behavior is to error
    on any mismatched IDs.
label1 : Str, optional
    Label for `distance_matrix` in the output visualization.
label2 : Str, optional
    Label for `metadata_distance_matrix` in the output visualization.

Returns
-------
metadata_distance_matrix : DistanceMatrix
    The Distance Matrix produced from the metadata column and used in the
    mantel test
mantel_scatter_visualization : Visualization
    Scatter plot rendering of the manteltest results