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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']
  --p-intersect-ids / --p-no-intersect-ids
                       If supplied, IDs that are not found in both the alpha
                       diversity vector and metadata will be discarded before
                       calculating the correlation. Default behavior is to
                       error on any mismatched IDs.           [default: False]
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.
intersect_ids : Bool, optional
    If supplied, IDs that are not found in both the alpha diversity vector
    and metadata will be discarded before calculating the correlation.
    Default behavior is to error on any mismatched IDs.

Returns
-------
visualization : Visualization