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adonis: adonis PERMANOVA test for beta group significance

Citations

  • Marti J Anderson. A new method for non-parametric multivariate analysis of variance. Austral ecology, 26(1):32–46, 2001. doi:https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x.

  • Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, and Helene Wagner. vegan: Community Ecology Package. 2018. R package version 2.5-3. URL: https://CRAN.R-project.org/package=vegan.

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_significance in that it accepts R formulae to
  perform multi-way ADONIS tests; beta_group_signficance only performs one-way
  tests. For more details, consult the reference manual available on the CRAN
  vegan page: https://CRAN.R-project.org/package=vegan

Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix       Matrix of distances between pairs of samples.
                                                                    [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple            Sample metadata containing formula terms.
     arguments will be
     merged)                                                        [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(1, None)       The number of permutations to be run when computing
                         p-values.                              [default: 999]
  --p-n-jobs NTHREADS    Number of parallel processes to run.     [default: 1]
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.

Import:

from qiime2.plugins.diversity.visualizers import adonis

Docstring:

adonis PERMANOVA test for beta 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_significance in that it accepts R formulae
to perform multi-way ADONIS tests; beta_group_signficance only performs
one-way tests. For more details, consult the reference manual available on
the CRAN vegan page: https://CRAN.R-project.org/package=vegan

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 : Threads, optional
    Number of parallel processes to run.

Returns
-------
visualization : Visualization