Docstring:
Usage: qiime diversity procrustes-analysis [OPTIONS]
Fit two ordination matrices with Procrustes analysis
Inputs:
--i-reference ARTIFACT The ordination matrix to which data is fitted to.
PCoAResults [required]
--i-other ARTIFACT The ordination matrix that's fitted to the
PCoAResults reference ordination. [required]
Parameters:
--p-dimensions INTEGER The number of dimensions to use when fitting the
Range(1, None) two matrices [default: 5]
--p-permutations VALUE Int % Range(1, None) | Str % Choices('disable')
The number of permutations to be run when computing
p-values. Supplying a value of `disable` will
disable permutation testing and p-values will not be
calculated (this results in *much* quicker execution
time if p-values are not desired). [default: 999]
Outputs:
--o-transformed-reference ARTIFACT
PCoAResults A normalized version of the "reference" ordination
matrix. [required]
--o-transformed-other ARTIFACT
PCoAResults A normalized and fitted version of the "other"
ordination matrix. [required]
--o-disparity-results ARTIFACT
ProcrustesStatistics The sum of the squares of the pointwise differences
between the two input datasets & its p value.
[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.
Import:
from qiime2.plugins.diversity.methods import procrustes_analysis
Docstring:
Procrustes Analysis
Fit two ordination matrices with Procrustes analysis
Parameters
----------
reference : PCoAResults
The ordination matrix to which data is fitted to.
other : PCoAResults
The ordination matrix that's fitted to the reference ordination.
dimensions : Int % Range(1, None), optional
The number of dimensions to use when fitting the two matrices
permutations : Int % Range(1, None) | Str % Choices('disable'), optional
The number of permutations to be run when computing p-values. Supplying
a value of `disable` will disable permutation testing and p-values will
not be calculated (this results in *much* quicker execution time if
p-values are not desired).
Returns
-------
transformed_reference : PCoAResults
A normalized version of the "reference" ordination matrix.
transformed_other : PCoAResults
A normalized and fitted version of the "other" ordination matrix.
disparity_results : ProcrustesStatistics
The sum of the squares of the pointwise differences between the two
input datasets & its p value.
