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