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ilr-phylogenetic-ordination: Ordination through a phylogenetic Isometric Log Ratio transform.ΒΆ

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).
  --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_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.