Fork me on GitHub

alpha: Alpha diversityΒΆ

Docstring:

Usage: qiime diversity alpha [OPTIONS]

  Computes a user-specified alpha diversity metric for all samples in a
  feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]   The feature table containing the samples for which
                       alpha diversity should be computed.          [required]
Parameters:
  --p-metric TEXT Choices('simpson_e', 'gini_index', 'doubles', 'ace',
    'margalef', 'shannon', 'mcintosh_e', 'strong', 'singles', 'heip_e', 'osd',
    'mcintosh_d', 'simpson', 'lladser_pe', 'brillouin_d', 'chao1',
    'dominance', 'chao1_ci', 'berger_parker_d', 'goods_coverage', 'enspie',
    'menhinick', 'kempton_taylor_q', 'michaelis_menten_fit',
    'observed_features', 'fisher_alpha', 'esty_ci', 'pielou_e', 'robbins')
                       The alpha diversity metric to be computed.   [required]
Outputs:
  --o-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
                       Vector containing per-sample alpha diversities.
                                                                    [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 alpha

Docstring:

Alpha diversity

Computes a user-specified alpha diversity metric for all samples in a
feature table.

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which alpha diversity
    should be computed.
metric : Str % Choices('mcintosh_e', 'esty_ci', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'menhinick', 'shannon', 'pielou_e', 'singles', 'simpson', 'chao1_ci', 'strong', 'fisher_alpha', 'osd', 'dominance', 'robbins', 'lladser_pe', 'kempton_taylor_q', 'mcintosh_d', 'brillouin_d', 'goods_coverage')
    The alpha diversity metric to be computed.

Returns
-------
alpha_diversity : SampleData[AlphaDiversity]
    Vector containing per-sample alpha diversities.