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('aitchison', 'braycurtis', 'canberra',
'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine',
'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'matching',
'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean',
'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')
The beta diversity metric to be computed. [required]
--p-pseudocount INTEGER A pseudocount to handle zeros for compositional
Range(1, None) metrics. This is ignored for other metrics.
[default: 1]
--p-n-jobs NTHREADS 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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. 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.
--example-data PATH Write example data 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('aitchison', 'braycurtis', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')
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 : Threads, 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.
