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.

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]
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 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