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.
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_features', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles')], optional
The metrics to be measured. By default computes observed_features,
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
