Docstring:
Usage: qiime diversity beta [OPTIONS]
Computes a user-specified beta diversity metric for all pairs of samples
in a feature table.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
PresenceAbsence] The feature table containing the samples over which
beta diversity should be computed. [required]
Parameters:
--p-metric TEXT Choices('rogerstanimoto', 'kulsinski', 'sokalmichener',
'dice', 'braycurtis', 'matching', 'canberra_adkins', 'jensenshannon',
'sqeuclidean', 'hamming', 'sokalsneath', 'canberra', 'chebyshev',
'seuclidean', 'aitchison', 'yule', 'cosine', 'correlation', 'minkowski',
'euclidean', 'russellrao', 'jaccard', 'cityblock')
The beta diversity metric to be computed. [required]
--p-pseudocount INTEGER
Range(1, None) A pseudocount to handle zeros for compositional
metrics. This is ignored for other metrics.
[default: 1]
--p-n-jobs VALUE Int % Range(1, None) | Str % Choices('auto')
The number of concurrent jobs to use in performing
this calculation. May not exceed the number of
available physical cores. If n-jobs = 'auto', one job
will be launched for each identified CPU core on the
host. [default: 1]
Outputs:
--o-distance-matrix ARTIFACT
DistanceMatrix The resulting distance matrix. [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 beta
Docstring:
Beta diversity
Computes a user-specified beta diversity metric for all pairs of samples in
a feature table.
Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
The feature table containing the samples over which beta diversity
should be computed.
metric : Str % Choices('kulsinski', 'seuclidean', 'sokalmichener', 'hamming', 'cityblock', 'canberra', 'euclidean', 'matching', 'aitchison', 'sokalsneath', 'jensenshannon', 'chebyshev', 'braycurtis', 'yule', 'sqeuclidean', 'correlation', 'jaccard', 'minkowski', 'cosine', 'canberra_adkins', 'dice', 'rogerstanimoto', 'russellrao')
The beta diversity metric to be computed.
pseudocount : Int % Range(1, None), optional
A pseudocount to handle zeros for compositional metrics. This is
ignored for other metrics.
n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
The number of concurrent jobs to use in performing this calculation.
May not exceed the number of available physical cores. If n_jobs =
'auto', one job will be launched for each identified CPU core on the
host.
Returns
-------
distance_matrix : DistanceMatrix
The resulting distance matrix.
