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('dominance', 'simpson_e', 'heip_e', 'mcintosh_e',
'simpson', 'singles', 'doubles', 'margalef', 'chao1_ci', 'robbins',
'gini_index', 'shannon', 'brillouin_d', 'fisher_alpha', 'chao1',
'mcintosh_d', 'lladser_pe', 'observed_features', 'enspie',
'kempton_taylor_q', 'ace', 'michaelis_menten_fit', 'esty_ci', 'pielou_e',
'osd', 'berger_parker_d', 'menhinick', 'goods_coverage', 'strong')
The alpha diversity metric to be computed. Information
about specific metrics is available at
https://data.qiime2.org/a_diversity_metrics [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('chao1_ci', 'menhinick', 'dominance', 'strong', 'brillouin_d', 'robbins', 'heip_e', 'lladser_pe', 'fisher_alpha', 'osd', 'singles', 'enspie', 'esty_ci', 'doubles', 'margalef', 'ace', 'gini_index', 'berger_parker_d', 'mcintosh_e', 'mcintosh_d', 'chao1', 'goods_coverage', 'simpson', 'kempton_taylor_q', 'shannon', 'pielou_e', 'simpson_e', 'observed_features', 'michaelis_menten_fit')
The alpha diversity metric to be computed. Information about specific
metrics is available at https://data.qiime2.org/a_diversity_metrics
Returns
-------
alpha_diversity : SampleData[AlphaDiversity]
Vector containing per-sample alpha diversities.
