Docstring:
Usage: qiime diversity core-metrics [OPTIONS]
Applies a collection of diversity metrics (non-phylogenetic) to a feature
table.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
The feature table containing the samples over which
diversity metrics should be computed. [required]
Parameters:
--p-sampling-depth INTEGER
Range(1, None) The total frequency that each sample should be
rarefied to prior to computing diversity metrics.
[required]
--m-metadata-file METADATA...
(multiple The sample metadata to use in the emperor plots.
arguments will
be merged) [required]
--p-with-replacement / --p-no-with-replacement
Rarefy with replacement by sampling from the
multinomial distribution instead of rarefying without
replacement. [default: False]
--p-n-jobs VALUE Int % Range(1, None) | Str % Choices('auto')
[beta methods only] - The number of concurrent jobs to
use in performing this calculation. May not exceed the
number of available physical cores. If n-jobs = 'auto',
one job will be launched for each identified CPU core
on the host. [default: 1]
Outputs:
--o-rarefied-table ARTIFACT FeatureTable[Frequency]
The resulting rarefied feature table. [required]
--o-observed-features-vector ARTIFACT SampleData[AlphaDiversity]
Vector of Observed Features values by sample.
[required]
--o-shannon-vector ARTIFACT SampleData[AlphaDiversity]
Vector of Shannon diversity values by sample.
[required]
--o-evenness-vector ARTIFACT SampleData[AlphaDiversity]
Vector of Pielou's evenness values by sample.
[required]
--o-jaccard-distance-matrix ARTIFACT
DistanceMatrix Matrix of Jaccard distances between pairs of samples.
[required]
--o-bray-curtis-distance-matrix ARTIFACT
DistanceMatrix Matrix of Bray-Curtis distances between pairs of
samples. [required]
--o-jaccard-pcoa-results ARTIFACT
PCoAResults PCoA matrix computed from Jaccard distances between
samples. [required]
--o-bray-curtis-pcoa-results ARTIFACT
PCoAResults PCoA matrix computed from Bray-Curtis distances
between samples. [required]
--o-jaccard-emperor VISUALIZATION
Emperor plot of the PCoA matrix computed from Jaccard.
[required]
--o-bray-curtis-emperor VISUALIZATION
Emperor plot of the PCoA matrix computed from
Bray-Curtis. [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 core_metrics
Docstring:
Core diversity metrics (non-phylogenetic)
Applies a collection of diversity metrics (non-phylogenetic) to a feature
table.
Parameters
----------
table : FeatureTable[Frequency]
The feature table containing the samples over which diversity metrics
should be computed.
sampling_depth : Int % Range(1, None)
The total frequency that each sample should be rarefied to prior to
computing diversity metrics.
metadata : Metadata
The sample metadata to use in the emperor plots.
with_replacement : Bool, optional
Rarefy with replacement by sampling from the multinomial distribution
instead of rarefying without replacement.
n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
[beta methods only] - The number of concurrent jobs to use in
performing this calculation. May not exceed the number of available
physical cores. If n_jobs = 'auto', one job will be launched for each
identified CPU core on the host.
Returns
-------
rarefied_table : FeatureTable[Frequency]
The resulting rarefied feature table.
observed_features_vector : SampleData[AlphaDiversity]
Vector of Observed Features values by sample.
shannon_vector : SampleData[AlphaDiversity]
Vector of Shannon diversity values by sample.
evenness_vector : SampleData[AlphaDiversity]
Vector of Pielou's evenness values by sample.
jaccard_distance_matrix : DistanceMatrix
Matrix of Jaccard distances between pairs of samples.
bray_curtis_distance_matrix : DistanceMatrix
Matrix of Bray-Curtis distances between pairs of samples.
jaccard_pcoa_results : PCoAResults
PCoA matrix computed from Jaccard distances between samples.
bray_curtis_pcoa_results : PCoAResults
PCoA matrix computed from Bray-Curtis distances between samples.
jaccard_emperor : Visualization
Emperor plot of the PCoA matrix computed from Jaccard.
bray_curtis_emperor : Visualization
Emperor plot of the PCoA matrix computed from Bray-Curtis.
