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procrustes-plot: Visualize and Interact with a procrustes plot¶
Docstring:
Usage: qiime emperor procrustes-plot [OPTIONS]
Plot two procrustes-fitted matrices
Inputs:
--i-reference-pcoa ARTIFACT
PCoAResults The reference ordination matrix to be plotted.
[required]
--i-other-pcoa ARTIFACT
PCoAResults The "other" ordination matrix to be plotted (the one
that was fitted to the reference). [required]
--i-m2-stats ARTIFACT ProcrustesStatistics
The M^2 value of the procrustes analysis & its
associated p value. [optional]
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).
--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: procrustes plot
qiime emperor procrustes-plot \
--i-reference-pcoa bc-pcoa-result.qza \
--i-other-pcoa unw-pcoa-result.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization plot.qzv
Import:
from qiime2.plugins.emperor.visualizers import procrustes_plot
Docstring:
Visualize and Interact with a procrustes plot
Plot two procrustes-fitted matrices
Parameters
----------
reference_pcoa : PCoAResults
The reference ordination matrix to be plotted.
other_pcoa : PCoAResults
The "other" ordination matrix to be plotted (the one that was fitted to
the reference).
metadata : Metadata
The sample metadata.
m2_stats : ProcrustesStatistics, optional
The M^2 value of the procrustes analysis & its associated p value.
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