alpha-rarefaction: Alpha rarefaction curves¶

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('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_features', 'pielou_e', 'robbins', 'shannon', 'simpson',
    'simpson_e', 'singles')
                          The metrics to be measured. By default computes
                          observed_features, 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).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this action. If not provided, the default
                          cache under $TMP/qiime2/ will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --help                  Show this message and exit.