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procrustes-plot: Visualize and Interact with a procrustes plotΒΆ

Docstring:

Usage: qiime emperor procrustes-plot [OPTIONS]

  Plot two procrustes-fitted matrices

Inputs:
  --i-reference-pcoa ARTIFACT
    PCoAResults          The reference ordination matrix to be plotted.
                                                                    [required]
  --i-other-pcoa ARTIFACT
    PCoAResults          The "other" ordination matrix to be plotted (the one
                         that was fitted to the reference).         [required]
  --i-m2-stats ARTIFACT ProcrustesStatistics
                         The M^2 value of the procrustes analysis & its
                         associated p value.                        [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple            The sample metadata.
     arguments will be
     merged)                                                        [required]
  --p-custom-axes TEXT...
    List[Str]            Numeric sample metadata columns that should be
                         included as axes in the Emperor plot.      [optional]
  --p-ignore-missing-samples / --p-no-ignore-missing-samples
                         This will suppress the error raised when the
                         coordinates matrix contains samples that are not
                         present in the metadata. Samples without metadata are
                         included by setting all metadata values to: "This
                         sample has no metadata". This flag is only applied if
                         at least one sample is present in both the
                         coordinates matrix and the metadata. [default: False]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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.emperor.visualizers import procrustes_plot

Docstring:

Visualize and Interact with a procrustes plot

Plot two procrustes-fitted matrices

Parameters
----------
reference_pcoa : PCoAResults
    The reference ordination matrix to be plotted.
other_pcoa : PCoAResults
    The "other" ordination matrix to be plotted (the one that was fitted to
    the reference).
metadata : Metadata
    The sample metadata.
m2_stats : ProcrustesStatistics, optional
    The M^2 value of the procrustes analysis & its associated p value.
custom_axes : List[Str], optional
    Numeric sample metadata columns that should be included as axes in the
    Emperor plot.
ignore_missing_samples : Bool, optional
    This will suppress the error raised when the coordinates matrix
    contains samples that are not present in the metadata. Samples without
    metadata are included by setting all metadata values to: "This sample
    has no metadata". This flag is only applied if at least one sample is
    present in both the coordinates matrix and the metadata.

Returns
-------
visualization : Visualization