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bray-curtis: Bray-Curtis Dissimilarity

Citations
  • Thorvald Sørensen. A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on danish commons. Biol. Skr., 5:1–34, 1948.

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