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mantel: Apply the Mantel test to two distance matricesΒΆ

Citations

[diversity:mantel:Man67]Nathan Mantel. The detection of disease clustering and a generalized regression approach. Cancer research, 27(2 Part 1):209–220, 1967.
[diversity:mantel:Pea95]Karl Pearson. Note on regression and inheritance in the case of two parents. Proceedings of the Royal Society of London, 58:240–242, 1895.
[diversity:mantel:Spe04]Charles Spearman. The proof and measurement of association between two things. The American journal of psychology, 15(1):72–101, 1904.

Docstring:

Usage: qiime diversity mantel [OPTIONS]

  Apply a two-sided Mantel test to identify correlation between two distance
  matrices.

  Note: the directionality of the comparison has no bearing on the results.
  Thus, comparing distance matrix X to distance matrix Y is equivalent to
  comparing Y to X.

  Note: the order of samples within the two distance matrices does not need
  to be the same; the distance matrices will be reordered before applying
  the Mantel test.

  See the scikit-bio docs for more details about the Mantel test:

  http://scikit-
  bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html

Options:
  --i-dm1 ARTIFACT PATH DistanceMatrix
                                  Matrix of distances between pairs of
                                  samples.  [required]
  --i-dm2 ARTIFACT PATH DistanceMatrix
                                  Matrix of distances between pairs of
                                  samples.  [required]
  --p-method [pearson|spearman]   The correlation test to be applied in the
                                  Mantel test.  [default: spearman]
  --p-permutations INTEGER RANGE  The number of permutations to be run when
                                  computing p-values. Supplying a value of
                                  zero 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]
  --p-intersect-ids / --p-no-intersect-ids
                                  If supplied, IDs that are not found in both
                                  distance matrices will be discarded before
                                  applying the Mantel test. Default behavior
                                  is to error on any mismatched IDs.
                                  [default: False]
  --p-label1 TEXT                 Label for `dm1` in the output visualization.
                                  [default: Distance Matrix 1]
  --p-label2 TEXT                 Label for `dm2` in the output visualization.
                                  [default: Distance Matrix 2]
  --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 mantel

Docstring:

Apply the Mantel test to two distance matrices

Apply a two-sided Mantel test to identify correlation between two distance
matrices.  Note: the directionality of the comparison has no bearing on the
results. Thus, comparing distance matrix X to distance matrix Y is
equivalent to comparing Y to X.  Note: the order of samples within the two
distance matrices does not need to be the same; the distance matrices will
be reordered before applying the Mantel test.  See the scikit-bio docs for
more details about the Mantel test:  http://scikit-
bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html

Parameters
----------
dm1 : DistanceMatrix
    Matrix of distances between pairs of samples.
dm2 : DistanceMatrix
    Matrix of distances between pairs of samples.
method : Str % Choices({'pearson', 'spearman'}), optional
    The correlation test to be applied in the Mantel test.
permutations : Int % Range(0, None), optional
    The number of permutations to be run when computing p-values. Supplying
    a value of zero will disable permutation testing and p-values will not
    be calculated (this results in *much* quicker execution time if
    p-values are not desired).
intersect_ids : Bool, optional
    If supplied, IDs that are not found in both distance matrices will be
    discarded before applying the Mantel test. Default behavior is to error
    on any mismatched IDs.
label1 : Str, optional
    Label for `dm1` in the output visualization.
label2 : Str, optional
    Label for `dm2` in the output visualization.

Returns
-------
visualization : Visualization