Docstring:
Usage: qiime diversity-lib beta-passthrough [OPTIONS]
Computes a distance matrix for all pairs of samples in a feature table using
the scikit-bio implementation of the selected beta diversity metric.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
The feature table containing the samples over which
beta diversity should be computed. [required]
Parameters:
--p-metric TEXT Choices('aitchison', 'canberra', 'canberra_adkins',
'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean',
'hamming', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto',
'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean',
'yule') 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 non-compositional
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).
--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.
Examples:
# ### example: run on one core (by default)
qiime diversity-lib beta-passthrough \
--i-table feature-table.qza \
--p-metric euclidean \
--o-distance-matrix euclidean-dm.qza
# ### example: to run on n cores, replace 1 here with your preferred integer
qiime diversity-lib beta-passthrough \
--i-table feature-table.qza \
--p-metric euclidean \
--p-n-jobs 1 \
--o-distance-matrix euclidean-dm.qza
# ### example: use 'auto' to run on all of host system's available CPU cores
# A default pseudocount of 1 is added to feature counts. Pseudocount is
# ignored for non-compositional metrics.
qiime diversity-lib beta-passthrough \
--i-table feature-table.qza \
--p-metric aitchison \
--p-n-jobs auto \
--o-distance-matrix aitchison-dm.qza
# ### example: use 'pseudocount' to manually set a pseudocount for
# compositional metrics
qiime diversity-lib beta-passthrough \
--i-table feature-table.qza \
--p-metric aitchison \
--p-n-jobs auto \
--p-pseudocount 5 \
--o-distance-matrix aitchison-dm.qza
Import:
from qiime2.plugins.diversity_lib.methods import beta_passthrough
Docstring:
Beta Passthrough (non-phylogenetic)
Computes a distance matrix for all pairs of samples in a feature table
using the scikit-bio implementation of the selected beta diversity metric.
Parameters
----------
table : FeatureTable[Frequency]
The feature table containing the samples over which beta diversity
should be computed.
metric : Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', '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 non-compositional 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.
