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
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.
ignore_pcoa_features : Bool, optional
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.
Returns
-------
visualization : Visualization
