beta-correlation: Beta diversity correlation¶

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: 'Distance Matrix']
  --p-label2 TEXT         Label for `metadata-distance-matrix` in the output
                          visualization.                 [default: 'Metadata']
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).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --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.