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alpha-correlation: Alpha diversity correlation

Citations
  • Karl Pearson. Note on regression and inheritance in the case of two parents. Proceedings of the Royal Society of London, 58:240–242, 1895.

  • Charles Spearman. The proof and measurement of association between two things. The American journal of psychology, 15(1):72–101, 1904.

Docstring:

Usage: qiime diversity alpha-correlation [OPTIONS]

  Determine whether numeric sample metadata columns are correlated with
  alpha diversity.

Inputs:
  --i-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
                       Vector of alpha diversity values by sample.  [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple          The sample metadata.
     arguments will
     be merged)                                                     [required]
  --p-method TEXT Choices('spearman', 'pearson')
                       The correlation test to be applied.
                                                         [default: 'spearman']
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 alpha_correlation

Docstring:

Alpha diversity correlation

Determine whether numeric sample metadata columns are correlated with alpha
diversity.

Parameters
----------
alpha_diversity : SampleData[AlphaDiversity]
    Vector of alpha diversity values by sample.
metadata : Metadata
    The sample metadata.
method : Str % Choices('spearman', 'pearson'), optional
    The correlation test to be applied.

Returns
-------
visualization : Visualization