Docstring:
Usage: qiime gneiss ilr-phylogenetic-ordination [OPTIONS]
Compute an ILR ordination 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]
--p-top-k-var INTEGER The top k most variable balances. [default: 10]
--p-clades TEXT... The names of clades to focus on (overrides
List[Str] top-k-var). [optional]
Outputs:
--o-ordination ARTIFACT The resulting ordination from the ilr transform.
PCoAResults [required]
--o-bifurcated-tree ARTIFACT
Phylogeny[Rooted] Bifurcating phylogeny [required]
--o-clade-metadata ARTIFACT FeatureData[Differential]
Metadata specifying clade membership. [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_ordination
Docstring:
Ordination through a phylogenetic Isometric Log Ratio transform.
Compute an ILR ordination given a rooted phylogeny.
Parameters
----------
table : FeatureTable[Frequency | Composition]
The feature table containing the samples in which the ilr transform
will be performed.
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.
pseudocount : Float, optional
The value to add to zero counts in the feature table.
top_k_var : Int, optional
The top k most variable balances.
clades : List[Str], optional
The names of clades to focus on (overrides top-k-var).
Returns
-------
ordination : PCoAResults
The resulting ordination from the ilr transform.
bifurcated_tree : Phylogeny[Rooted]
Bifurcating phylogeny
clade_metadata : FeatureData[Differential]
Metadata specifying clade membership.
