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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.

Options:
  --i-biplot ARTIFACT PATH PCoAResults % Properties(['biplot'])
                                  The principal coordinates matrix to be
                                  plotted.  [required]
  --m-sample-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. The sample
                                  metadata  [required]
  --m-feature-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. The
                                  feature metadata (useful to manipulate the
                                  arrows in the 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]
  --p-number-of-features INTEGER RANGE
                                  The number of most important features
                                  (arrows) to display in the ordination.
                                  [default: 5]
  --o-visualization VISUALIZATION PATH
                                  [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.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