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alpha-rarefaction: Alpha rarefaction curvesΒΆ

Docstring:

Usage: qiime diversity alpha-rarefaction [OPTIONS]

  Generate interactive alpha rarefaction curves by computing rarefactions
  between `min_depth` and `max_depth`. The number of intermediate depths to
  compute is controlled by the `steps` parameter, with n `iterations` being
  computed at each rarefaction depth. If sample metadata is provided,
  samples may be grouped based on distinct values within a metadata column.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          Feature table to compute rarefaction curves from.
                                                                    [required]
  --i-phylogeny ARTIFACT  Optional phylogeny for phylogenetic metrics.
    Phylogeny[Rooted]                                               [optional]
Parameters:
  --p-max-depth INTEGER   The maximum rarefaction depth. Must be greater than
    Range(1, None)        min-depth.                                [required]
  --p-metrics TEXT... Choices('enspie', 'simpson_e',
    'michaelis_menten_fit', 'margalef', 'singles', 'simpson', 'chao1',
    'heip_e', 'doubles', 'mcintosh_d', 'ace', 'menhinick', 'faith_pd',
    'shannon', 'fisher_alpha', 'brillouin_d', 'lladser_pe', 'observed_otus',
    'mcintosh_e', 'pielou_e', 'robbins', 'berger_parker_d', 'goods_coverage',
    'gini_index', 'dominance')
                          The metrics to be measured. By default computes
                          observed_otus, shannon, and if phylogeny is
                          provided, faith_pd.                       [optional]
  --m-metadata-file METADATA...
    (multiple arguments   The sample metadata.
     will be merged)                                                [optional]
  --p-min-depth INTEGER   The minimum rarefaction depth.
    Range(1, None)                                                [default: 1]
  --p-steps INTEGER       The number of rarefaction depths to include between
    Range(2, None)        min-depth and max-depth.               [default: 10]
  --p-iterations INTEGER  The number of rarefied feature tables to compute at
    Range(1, None)        each step.                             [default: 10]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.diversity.visualizers import alpha_rarefaction

Docstring:

Alpha rarefaction curves

Generate interactive alpha rarefaction curves by computing rarefactions
between `min_depth` and `max_depth`. The number of intermediate depths to
compute is controlled by the `steps` parameter, with n `iterations` being
computed at each rarefaction depth. If sample metadata is provided, samples
may be grouped based on distinct values within a metadata column.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to compute rarefaction curves from.
max_depth : Int % Range(1, None)
    The maximum rarefaction depth. Must be greater than min_depth.
phylogeny : Phylogeny[Rooted], optional
    Optional phylogeny for phylogenetic metrics.
metrics : Set[Str % Choices('dominance', 'goods_coverage', 'michaelis_menten_fit', 'observed_otus', 'doubles', 'shannon', 'chao1', 'fisher_alpha', 'simpson', 'lladser_pe', 'ace', 'mcintosh_d', 'pielou_e', 'gini_index', 'heip_e', 'faith_pd', 'berger_parker_d', 'margalef', 'mcintosh_e', 'menhinick', 'robbins', 'singles', 'simpson_e', 'brillouin_d', 'enspie')], optional
    The metrics to be measured. By default computes observed_otus, shannon,
    and if phylogeny is provided, faith_pd.
metadata : Metadata, optional
    The sample metadata.
min_depth : Int % Range(1, None), optional
    The minimum rarefaction depth.
steps : Int % Range(2, None), optional
    The number of rarefaction depths to include between min_depth and
    max_depth.
iterations : Int % Range(1, None), optional
    The number of rarefied feature tables to compute at each step.

Returns
-------
visualization : Visualization