biplot: Visualize and Interact with Principal Coordinates Analysis Biplot¶

Docstring:

Usage: qiime emperor biplot [OPTIONS]

  Generates an interactive ordination biplot where the user can visually
  integrate sample and feature metadata. Vectors representing the n most
  important features are then plotted in the emperor visualization (5 largest,
  by default).

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
     arguments will be   arrows in the plot).
     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-invert / --p-no-invert
                         If specified, the point and arrow coordinates will
                         be swapped.                          [default: False]
  --p-number-of-features INTEGER
    Range(1, None)       The number of most important features (arrows) to
                         display in the ordination. “Importance” is calculated
                         for each feature based on the vector’s magnitude
                         (euclidean distance from origin).        [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).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.