Docstring:
Usage: qiime diversity adonis [OPTIONS]
Determine whether groups of samples are significantly different from one
another using the ADONIS permutation-based statistical test in vegan-R.
The function partitions sums of squares of a multivariate data set, and is
directly analogous to MANOVA (multivariate analysis of variance). This
action differs from beta_group_signficance in that it accepts R formulae
to perform multi-way ADONIS tests; beta_group_signficance only performs
one-way tests. For more details see
http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
Options:
--i-distance-matrix ARTIFACT PATH DistanceMatrix
Matrix of distances between pairs of
samples. [required]
--m-metadata-file MULTIPLE FILE
Metadata file or artifact viewable as
metadata. This option may be supplied
multiple times to merge metadata. Sample
metadata containing formula terms.
[required]
--p-formula TEXT Model formula containing only independent
terms contained in the sample metadata.
These can be continuous variables or
factors, and they can have interactions as
in a typical R formula. E.g., the formula
"treatment+block" would test whether the
input distance matrix partitions based on
"treatment" and "block" sample metadata. The
formula "treatment*block" would test both of
those effects as well as their interaction.
Enclose formulae in quotes to avoid
unpleasant surprises. [required]
--p-permutations INTEGER RANGE The number of permutations to be run when
computing p-values. [default: 999]
--p-n-jobs INTEGER RANGE Number of parallel processes to run.
[default: 1]
--o-visualization VISUALIZATION PATH
[required if not passing --output-dir]
--output-dir DIRECTORY Output unspecified results to a directory
--cmd-config FILE Use config file for command options
--verbose Display verbose output to stdout and/or
stderr during execution of this action.
[default: False]
--quiet Silence output if execution is successful
(silence is golden). [default: False]
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.diversity.visualizers import adonis
Docstring:
Beta diversity group significance
Determine whether groups of samples are significantly different from one
another using the ADONIS permutation-based statistical test in vegan-R. The
function partitions sums of squares of a multivariate data set, and is
directly analogous to MANOVA (multivariate analysis of variance). This
action differs from beta_group_signficance in that it accepts R formulae to
perform multi-way ADONIS tests; beta_group_signficance only performs one-
way tests. For more details see
http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
Parameters
----------
distance_matrix : DistanceMatrix
Matrix of distances between pairs of samples.
metadata : Metadata
Sample metadata containing formula terms.
formula : Str
Model formula containing only independent terms contained in the sample
metadata. These can be continuous variables or factors, and they can
have interactions as in a typical R formula. E.g., the formula
"treatment+block" would test whether the input distance matrix
partitions based on "treatment" and "block" sample metadata. The
formula "treatment*block" would test both of those effects as well as
their interaction. Enclose formulae in quotes to avoid unpleasant
surprises.
permutations : Int % Range(1, None), optional
The number of permutations to be run when computing p-values.
n_jobs : Int % Range(1, None), optional
Number of parallel processes to run.
Returns
-------
visualization : Visualization