Fork me on GitHub

alpha-correlation: Alpha diversity correlation

Citations

[diversity:alpha-correlation:Pea95]Karl Pearson. Note on regression and inheritance in the case of two parents. Proceedings of the Royal Society of London, 58:240–242, 1895.
[diversity:alpha-correlation:Spe04]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.

Options:
  --i-alpha-diversity ARTIFACT PATH SampleData[AlphaDiversity]
                                  Vector of alpha diversity values by sample.
                                  [required]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. The sample
                                  metadata.  [required]
  --p-method [pearson|spearman]   The correlation test to be applied.
                                  [default: spearman]
  --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 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({'pearson', 'spearman'}), optional
    The correlation test to be applied.

Returns
-------
visualization : Visualization