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 arrows
arguments will in the plot).
be 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.
--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. Vectors representing the n most
important features are then plotted in the emperor visualization (5
largest, by default).
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.
invert : Bool, optional
If specified, the point and arrow coordinates will be swapped.
number_of_features : Int % Range(1, None), optional
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).
Returns
-------
visualization : Visualization
