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).
--example-data PATH Write example data 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.
