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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  Feature table to compute rarefaction curves
                                  from.  [required]
  --p-max-depth INTEGER RANGE     The maximum rarefaction depth. Must be
                                  greater than min_depth.  [required]
  --i-phylogeny ARTIFACT PATH Phylogeny[Rooted]
                                  Optional phylogeny for phylogenetic metrics.
                                  [optional]
  --p-metrics MULTIPLE [faith_pd|dominance|enspie|mcintosh_e|singles|chao1|goods_coverage|berger_parker_d|robbins|michaelis_menten_fit|menhinick|pielou_e|fisher_alpha|ace|gini_index|mcintosh_d|simpson_e|shannon|observed_otus|simpson|lladser_pe|doubles|brillouin_d|margalef|heip_e]
                                  The metrics to be measured. By default
                                  computes observed_otus, shannon, and if
                                  phylogeny is provided, faith_pd.  [optional]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. The sample
                                  metadata.  [optional]
  --p-min-depth INTEGER RANGE     The minimum rarefaction depth.  [default: 1]
  --p-steps INTEGER RANGE         The number of rarefaction depths to include
                                  between min_depth and max_depth.  [default:
                                  10]
  --p-iterations INTEGER RANGE    The number of rarefied feature tables to
                                  compute at each step.  [default: 10]
  --o-visualization VISUALIZATION PATH
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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({'ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'dominance', 'doubles', 'enspie', 'faith_pd', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_otus', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles'})], 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