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correlation-clustering: Hierarchical clustering using feature correlation.ΒΆ

Docstring:

Usage: qiime gneiss correlation-clustering [OPTIONS]

  Build a bifurcating tree that represents a hierarchical clustering of
  features.  The hiearchical clustering uses Ward hierarchical clustering
  based on the degree of proportionality between features.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table containing the samples in which
                          the columns will be clustered.            [required]
Parameters:
  --p-pseudocount NUMBER  The value to add to zero counts in the feature
                          table.                                [default: 0.5]
Outputs:
  --o-clustering ARTIFACT A hierarchy of feature identifiers where each tip
    Hierarchy             corresponds to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [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.gneiss.methods import correlation_clustering

Docstring:

Hierarchical clustering using feature correlation.

Build a bifurcating tree that represents a hierarchical clustering of
features.  The hiearchical clustering uses Ward hierarchical clustering
based on the degree of proportionality between features.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples in which the columns will be
    clustered.
pseudocount : Float, optional
    The value to add to zero counts in the feature table.

Returns
-------
clustering : Hierarchy
    A hierarchy of feature identifiers where each tip corresponds to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.