Fork me on GitHub

core-metrics-phylogenetic: Core diversity metrics (phylogenetic and non-phylogenetic)ΒΆ

Docstring:

Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]

  Applies a collection of diversity metrics (both phylogenetic and 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]
  --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-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 arguments   The sample metadata to use in the emperor plots.
     will be merged)                                                [required]
  --p-n-jobs-or-threads VALUE Int % Range(1, None) | Str % Choices('auto')
                          [beta/beta-phylogenetic methods only] - The number
                          of concurrent jobs or CPU threads to use in
                          performing this calculation. Individual methods will
                          create jobs/threads as implemented in
                          q2-diversity-lib dependencies. May not exceed the
                          number of available physical cores. If
                          n-jobs-or-threads = 'auto', one thread/job will be
                          created for each identified CPU core on the host.
                                                                  [default: 1]
Outputs:
  --o-rarefied-table ARTIFACT FeatureTable[Frequency]
                          The resulting rarefied feature table.     [required]
  --o-faith-pd-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Faith PD values by sample.      [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-unweighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of unweighted UniFrac distances between
                          pairs of samples.                         [required]
  --o-weighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of weighted UniFrac distances between pairs
                          of samples.                               [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-unweighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from unweighted UniFrac
                          distances between samples.                [required]
  --o-weighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from weighted UniFrac
                          distances between 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-unweighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          unweighted UniFrac.                       [required]
  --o-weighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          weighted UniFrac.                         [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).
  --examples              Show usage examples and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.diversity.pipelines import core_metrics_phylogenetic

Docstring:

Core diversity metrics (phylogenetic and non-phylogenetic)

Applies a collection of diversity metrics (both phylogenetic and non-
phylogenetic) to a feature table.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples over which diversity metrics
    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.
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.
n_jobs_or_threads : Int % Range(1, None) | Str % Choices('auto'), optional
    [beta/beta-phylogenetic methods only] - The number of concurrent jobs
    or CPU threads to use in performing this calculation. Individual
    methods will create jobs/threads as implemented in q2-diversity-lib
    dependencies. May not exceed the number of available physical cores. If
    n_jobs_or_threads = 'auto', one thread/job will be created for each
    identified CPU core on the host.

Returns
-------
rarefied_table : FeatureTable[Frequency]
    The resulting rarefied feature table.
faith_pd_vector : SampleData[AlphaDiversity]
    Vector of Faith PD values by sample.
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.
unweighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of unweighted UniFrac distances between pairs of samples.
weighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of weighted UniFrac distances between pairs of samples.
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.
unweighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from unweighted UniFrac distances between samples.
weighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from weighted UniFrac distances between 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.
unweighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from unweighted UniFrac.
weighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from weighted UniFrac.
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.