ilr-phylogenetic: Isometric Log-ratio Transform applied to a phylogenetic tree¶

Docstring:

Usage: qiime gneiss ilr-phylogenetic [OPTIONS]

  Calculate balances given a rooted phylogeny.

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 rooted phylogeny of feature identifiers that
    Phylogeny[Rooted]     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. This tree may contain polytomic nodes (i.e.,
                          nodes with more than two children), in which case
                          they will be bifurcated.                  [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]
  --o-hierarchy ARTIFACT  Hierarchy from bifurcated phylogeny
    Hierarchy                                                       [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.
  --help                  Show this message and exit.