Docstring:
Usage: qiime diversity alpha-phylogenetic [OPTIONS]
Computes a user-specified phylogenetic alpha diversity metric for all
samples in a feature table.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
PresenceAbsence] The feature table containing the samples for which
alpha diversity should be computed. [required]
--i-phylogeny ARTIFACT Phylogenetic tree containing tip identifiers that
Phylogeny[Rooted] correspond 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. [required]
Parameters:
--p-metric TEXT The alpha diversity metric to be computed.
Choices('faith_pd') [required]
Outputs:
--o-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
Vector containing per-sample alpha diversities.
[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.diversity.pipelines import alpha_phylogenetic
Docstring:
Alpha diversity (phylogenetic)
Computes a user-specified phylogenetic alpha diversity metric for all
samples in a feature table.
Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
The feature table containing the samples for which alpha diversity
should be computed.
phylogeny : Phylogeny[Rooted]
Phylogenetic tree containing tip identifiers that correspond 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.
metric : Str % Choices('faith_pd')
The alpha diversity metric to be computed.
Returns
-------
alpha_diversity : SampleData[AlphaDiversity]
Vector containing per-sample alpha diversities.
