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procrustes-analysis: Procrustes AnalysisΒΆ

Docstring:

Usage: qiime diversity procrustes-analysis [OPTIONS]

  Fit two ordination matrices with Procrustes analysis

Inputs:
  --i-reference ARTIFACT  The ordination matrix to which data is fitted to.
    PCoAResults                                                     [required]
  --i-other ARTIFACT      The ordination matrix that's fitted to the
    PCoAResults           reference ordination.                     [required]
Parameters:
  --p-dimensions INTEGER  The number of dimensions to use when fitting the
    Range(1, None)        two matrices                            [default: 5]
  --p-permutations VALUE Int % Range(1, None) | Str % Choices('disable')
                          The number of permutations to be run when computing
                          p-values. Supplying a value of `disable` will
                          disable permutation testing and p-values will not be
                          calculated (this results in *much* quicker execution
                          time if p-values are not desired).    [default: 999]
Outputs:
  --o-transformed-reference ARTIFACT
    PCoAResults           A normalized version of the "reference" ordination
                          matrix.                                   [required]
  --o-transformed-other ARTIFACT
    PCoAResults           A normalized and fitted version of the "other"
                          ordination matrix.                        [required]
  --o-disparity-results ARTIFACT
    ProcrustesStatistics  The sum of the squares of the pointwise differences
                          between the two input datasets & its p value.
                                                                    [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).
  --examples              Show usage examples and exit.
  --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
    The number of dimensions to use when fitting the two matrices
permutations : Int % Range(1, None) | Str % Choices('disable'), optional
    The number of permutations to be run when computing p-values. Supplying
    a value of `disable` will disable permutation testing and p-values will
    not be calculated (this results in *much* quicker execution time if
    p-values are not desired).

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.
disparity_results : ProcrustesStatistics
    The sum of the squares of the pointwise differences between the two
    input datasets & its p value.