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beta-group-significance: Beta diversity group significance

Citations

[diversity:beta-group-significance:And01]Marti J Anderson. A new method for non-parametric multivariate analysis of variance. Austral ecology, 26(1):32–46, 2001. doi:https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x.

Docstring:

Usage: qiime diversity beta-group-significance [OPTIONS]

  Determine whether groups of samples are significantly different from one
  another using a permutation-based statistical test.

Options:
  --i-distance-matrix ARTIFACT PATH DistanceMatrix
                                  Matrix of distances between pairs of
                                  samples.  [required]
  --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[Categorical]
                                  Column from metadata file or artifact
                                  viewable as metadata. Categorical sample
                                  metadata column.  [required]
  --p-method [permanova|anosim|permdisp]
                                  The group significance test to be applied.
                                  [default: permanova]
  --p-pairwise / --p-no-pairwise  Perform pairwise tests between all pairs of
                                  groups in addition to the test across all
                                  groups. This can be very slow if there are a
                                  lot of groups in the metadata column.
                                  [default: False]
  --p-permutations INTEGER        The number of permutations to be run when
                                  computing p-values.  [default: 999]
  --o-visualization VISUALIZATION PATH
                                  [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.visualizers import beta_group_significance

Docstring:

Beta diversity group significance

Determine whether groups of samples are significantly different from one
another using a permutation-based statistical test.

Parameters
----------
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
metadata : MetadataColumn[Categorical]
    Categorical sample metadata column.
method : Str % Choices({'anosim', 'permanova', 'permdisp'}), optional
    The group significance test to be applied.
pairwise : Bool, optional
    Perform pairwise tests between all pairs of groups in addition to the
    test across all groups. This can be very slow if there are a lot of
    groups in the metadata column.
permutations : Int, optional
    The number of permutations to be run when computing p-values.

Returns
-------
visualization : Visualization