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/skbio.stats.distance.mantel
Inputs:
--i-dm1 ARTIFACT Matrix of distances between pairs of samples.
DistanceMatrix [required]
--i-dm2 ARTIFACT Matrix of distances between pairs of samples.
DistanceMatrix [required]
Parameters:
--p-method TEXT Choices('spearman', 'pearson')
The correlation test to be applied in the Mantel
test. [default: 'spearman']
--p-permutations INTEGER
Range(0, None) 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']
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 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/skbio.stats.distance.mantel
Parameters
----------
dm1 : DistanceMatrix
Matrix of distances between pairs of samples.
dm2 : DistanceMatrix
Matrix of distances between pairs of samples.
method : Str % Choices('spearman', 'pearson'), 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
