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ilr-hierarchical: Isometric Log-ratio Transform applied to a hierarchical clusteringΒΆ

Docstring:

Usage: qiime gneiss ilr-hierarchical [OPTIONS]

  Calculate balances given a hierarchy.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | Composition]
                          The feature table containing the samples in which
                          the ilr transform will be performed.      [required]
  --i-tree ARTIFACT       A hierarchy of feature identifiers that defines the
    Hierarchy             partitions of features.  Each tip in the
                          hierarchycorresponds 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.  This assumes
                          that all of the internal nodes in the tree have
                          labels.                                   [required]
Parameters:
  --p-pseudocount NUMBER  The value to add to zero counts in the feature
                          table.                                [default: 0.5]
Outputs:
  --o-balances ARTIFACT FeatureTable[Balance]
                          The resulting balances from the ilr transform.
                                                                    [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 ilr_hierarchical

Docstring:

Isometric Log-ratio Transform applied to a hierarchical clustering

Calculate balances given a hierarchy.

Parameters
----------
table : FeatureTable[Frequency | Composition]
    The feature table containing the samples in which the ilr transform
    will be performed.
tree : Hierarchy
    A hierarchy of feature identifiers that defines the partitions of
    features.  Each tip in the hierarchycorresponds 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.  This assumes that all of the internal nodes in the tree
    have labels.
pseudocount : Float, optional
    The value to add to zero counts in the feature table.

Returns
-------
balances : FeatureTable[Balance]
    The resulting balances from the ilr transform.