Fork me on GitHub

procrustes-analysis: Procrustes AnalysisΒΆ

Docstring:

Usage: qiime diversity procrustes-analysis [OPTIONS]

  Fit two ordination matrices with Procrustes analysis

Options:
  --i-reference ARTIFACT PATH PCoAResults
                                  The ordination matrix to which data is
                                  fitted to.  [required]
  --i-other ARTIFACT PATH PCoAResults
                                  The ordination matrix that's fitted to the
                                  reference ordination.  [required]
  --p-dimensions INTEGER RANGE    [default: 5]
  --o-transformed-reference ARTIFACT PATH PCoAResults
                                  A normalized version of the "reference"
                                  ordination matrix.  [required if not passing
                                  --output-dir]
  --o-transformed-other ARTIFACT PATH PCoAResults
                                  A normalized and fitted version of the
                                  "other" ordination matrix.  [required if not
                                  passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.diversity.methods import procrustes_analysis

Docstring:

Procrustes Analysis

Fit two ordination matrices with Procrustes analysis

Parameters
----------
reference : PCoAResults
    The ordination matrix to which data is fitted to.
other : PCoAResults
    The ordination matrix that's fitted to the reference ordination.
dimensions : Int % Range(1, None), optional

Returns
-------
transformed_reference : PCoAResults
    A normalized version of the "reference" ordination matrix.
transformed_other : PCoAResults
    A normalized and fitted version of the "other" ordination matrix.