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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.

Options:
  --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[Numeric]
                                  Column from metadata file or artifact
                                  viewable as metadata. Numeric metadata
                                  column from which to compute pairwise
                                  Euclidean distances  [required]
  --i-distance-matrix ARTIFACT PATH DistanceMatrix
                                  Matrix of distances between pairs of
                                  samples.  [required]
  --p-method [pearson|spearman]   The correlation test to be applied in the
                                  Mantel test.  [default: spearman]
  --p-permutations INTEGER RANGE  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]
  --o-metadata-distance-matrix ARTIFACT PATH DistanceMatrix
                                  The Distance Matrix produced from the
                                  metadata column and used in the mantel test
                                  [required if not passing --output-dir]
  --o-mantel-scatter-visualization VISUALIZATION PATH
                                  Scatter plot rendering of the manteltest
                                  results  [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.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({'pearson', 'spearman'}), 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