Fork me on GitHub

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]
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).
  --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.
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