Fork me on GitHub

plot: Visualize and Interact with Principal Coordinates Analysis PlotsΒΆ

Docstring:

Usage: qiime emperor plot [OPTIONS]

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

Options:
  --i-pcoa ARTIFACT PATH PCoAResults
                                  The principal coordinates matrix to be
                                  plotted.  [required]
  --m-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]
  --p-custom-axes MULTIPLE TEXT   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]
  --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 plot

Docstring:

Visualize and Interact with Principal Coordinates Analysis Plots

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

Parameters
----------
pcoa : PCoAResults
    The principal coordinates matrix to be plotted.
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