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bray-curtis: Bray-Curtis Dissimilarity¶
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Docstring:
Usage: qiime diversity-lib bray-curtis [OPTIONS]
Compute Bray-Curtis dissimilarity for each sample in a feature table. Note:
Frequency and relative frequency data produce different results unless
overall sample sizes are identical. Please consider the impact on your
results if you use Bray-Curtis with count data that has not been adjusted
(normalized).
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency]
The feature table containing the samples for which
Bray-Curtis dissimilarity should be computed.
[required]
Parameters:
--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 Distance matrix for Bray-Curtis dissimilarity
[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 bray-curtis \
--i-table feature-table.qza \
--o-distance-matrix bray-curtis-dm.qza
# ### example: to run on n cores, replace 1 here with your preferred integer
qiime diversity-lib bray-curtis \
--i-table feature-table.qza \
--p-n-jobs 1 \
--o-distance-matrix bray-curtis-dm.qza
# ### example: use 'auto' to run on all of host system's available CPU cores
qiime diversity-lib bray-curtis \
--i-table feature-table.qza \
--p-n-jobs auto \
--o-distance-matrix bray-curtis-dm.qza
Import:
from qiime2.plugins.diversity_lib.methods import bray_curtis
Docstring:
Bray-Curtis Dissimilarity
Compute Bray-Curtis dissimilarity for each sample in a feature table. Note:
Frequency and relative frequency data produce different results unless
overall sample sizes are identical. Please consider the impact on your
results if you use Bray-Curtis with count data that has not been adjusted
(normalized).
Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency]
The feature table containing the samples for which Bray-Curtis
dissimilarity should be computed.
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
Distance matrix for Bray-Curtis dissimilarity