plot: Visualize and Interact with Principal Coordinates Analysis Plots¶

Docstring:

Usage: qiime emperor plot [OPTIONS]

  Generates an interactive ordination plot where the user can visually
  integrate sample metadata.

Inputs:
  --i-pcoa ARTIFACT      The principal coordinates matrix to be plotted.
    PCoAResults                                                     [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]
  --p-ignore-pcoa-features / --p-no-ignore-pcoa-features
                         Biplot arrows cannot be visualized using this
                         method. If you want to visualize biplot arrows use
                         the `biplot` method. Enabling this setting will
                         ignore any PCoA features that are present, otherwise,
                         if PCoA features are detected an error will be
                         raised.                              [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).
  --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.

Examples:
  # ### example: emperor plot
  qiime emperor plot \
    --i-pcoa pcoa-result.qza \
    --m-metadata-file sample-metadata.tsv \
    --o-visualization plot.qzv