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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Composition | Frequency]
                                  The feature table containing the samples in
                                  which the ilr transform will be performed.
                                  [required]
  --i-tree ARTIFACT PATH 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.  [required]
  --p-pseudocount FLOAT           The value to add to zero counts in the
                                  feature table.  [default: 0.5]
  --o-balances ARTIFACT PATH FeatureTable[Balance]
                                  The resulting balances from the ilr
                                  transform.  [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.gneiss.methods import ilr_hierarchical

Docstring:

Isometric Log-ratio Transform applied to a hierarchical clustering

Calculate balances given a hierarchy.

Parameters
----------
table : FeatureTable[Composition | Frequency]
    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.