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pcoa-biplot: Principal Coordinate Analysis BiplotΒΆ

Citations

[diversity:pcoa-biplot:LL12]Pierre Legendre and Louis Legendre. Numerical Ecology, pages 499. Elsevier, Third edition, 2012.

Docstring:

Usage: qiime diversity pcoa-biplot [OPTIONS]

  Project features into a principal coordinates matrix. The features used
  should be the features used to compute the distance matrix. It is
  recommended that these variables be normalized in cases of dimensionally
  heterogeneous physical variables.

Options:
  --i-pcoa ARTIFACT PATH PCoAResults
                                  The PCoA where the features will be
                                  projected onto.  [required]
  --i-features ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  Variables to project onto the PCoA matrix
                                  [required]
  --o-biplot ARTIFACT PATH PCoAResults % Properties(['biplot'])
                                  The resulting PCoA 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 pcoa_biplot

Docstring:

Principal Coordinate Analysis Biplot

Project features into a principal coordinates matrix. The features used
should be the features used to compute the distance matrix. It is
recommended that these variables be normalized in cases of dimensionally
heterogeneous physical variables.

Parameters
----------
pcoa : PCoAResults
    The PCoA where the features will be projected onto.
features : FeatureTable[RelativeFrequency]
    Variables to project onto the PCoA matrix

Returns
-------
biplot : PCoAResults % Properties(['biplot'])
    The resulting PCoA matrix.