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alpha-correlation: Alpha diversity correlation

Citations

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).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.

Examples:
  # ### example: alpha correlation faith pd
  qiime diversity alpha-correlation \
    --i-alpha-diversity alpha-div-faith-pd.qza \
    --m-metadata-file metadata.tsv \
    --o-visualization visualization.qzv

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