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ilr-phylogenetic-differential: Differentially abundant Phylogenetic Log Ratios.ΒΆ

Docstring:

Usage: qiime gneiss ilr-phylogenetic-differential [OPTIONS]

  Compute an ILR transform of differentials given a rooted phylogeny.

Inputs:
  --i-differential ARTIFACT FeatureData[Differential]
                       The differential abundance results in which will be
                       ilr transformed.                             [required]
  --i-tree ARTIFACT    A rooted phylogeny of feature identifiers that defines
    Phylogeny[Rooted]  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]
Outputs:
  --o-ilr-differential ARTIFACT FeatureData[Differential]
                       Per clade differential abundance results.    [required]
  --o-bifurcated-tree ARTIFACT
    Phylogeny[Rooted]  Bifurcating phylogeny.                       [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).
  --examples           Show usage examples and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.

Import:

from qiime2.plugins.gneiss.methods import ilr_phylogenetic_differential

Docstring:

Differentially abundant Phylogenetic Log Ratios.

Compute an ILR transform of differentials given a rooted phylogeny.

Parameters
----------
differential : FeatureData[Differential]
    The differential abundance results in which will be ilr transformed.
tree : Phylogeny[Rooted]
    A rooted phylogeny 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. This tree may contain polytomic nodes (i.e., nodes with
    more than two children), in which case they will be bifurcated.

Returns
-------
ilr_differential : FeatureData[Differential]
    Per clade differential abundance results.
bifurcated_tree : Phylogeny[Rooted]
    Bifurcating phylogeny.