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biplot: Visualize and Interact with Principal Coordinates Analysis BiplotΒΆ

Docstring:

Usage: qiime emperor biplot [OPTIONS]

  Generates an interactive ordination biplot where the user can visually
  integrate sample and feature metadata.

Inputs:
  --i-biplot ARTIFACT PCoAResults % Properties('biplot')
                       The principal coordinates matrix to be plotted.
                                                                    [required]
Parameters:
  --m-sample-metadata-file METADATA...
    (multiple          The sample metadata
     arguments will
     be merged)                                                     [required]
  --m-feature-metadata-file METADATA...
    (multiple          The feature metadata (useful to manipulate the arrows
     arguments will    in the plot).
     be merged)                                                     [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]
  --p-number-of-features INTEGER
    Range(1, None)     The number of most important features (arrows) to
                       display in the ordination.                 [default: 5]
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 biplot

Docstring:

Visualize and Interact with Principal Coordinates Analysis Biplot

Generates an interactive ordination biplot where the user can visually
integrate sample and feature metadata.

Parameters
----------
biplot : PCoAResults % Properties('biplot')
    The principal coordinates matrix to be plotted.
sample_metadata : Metadata
    The sample metadata
feature_metadata : Metadata, optional
    The feature metadata (useful to manipulate the arrows in the 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.
number_of_features : Int % Range(1, None), optional
    The number of most important features (arrows) to display in the
    ordination.

Returns
-------
visualization : Visualization