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bioenv: bioenv

Citations
  • KR Clarke and M Ainsworth. A method of linking multivariate community structure to environmental variables. Marine ecology progress series, pages 205–219, 1993.

Docstring:

Usage: qiime diversity bioenv [OPTIONS]

  Find the subsets of variables in metadata whose Euclidean distances are
  maximally rank-correlated with distance matrix. All numeric variables in
  metadata will be considered, and samples which are missing data will be
  dropped. The output visualization will indicate how many samples were
  dropped due to missing data, if any were dropped.

Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix     Matrix of distances between pairs of samples.
                                                                    [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple          The sample metadata.
     arguments will
     be merged)                                                     [required]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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.visualizers import bioenv

Docstring:

bioenv

Find the subsets of variables in metadata whose Euclidean distances are
maximally rank-correlated with distance matrix. All numeric variables in
metadata will be considered, and samples which are missing data will be
dropped. The output visualization will indicate how many samples were
dropped due to missing data, if any were dropped.

Parameters
----------
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
metadata : Metadata
    The sample metadata.

Returns
-------
visualization : Visualization