Docstring:
Usage: qiime diversity beta-correlation [OPTIONS]
Create a distance matrix from a numeric metadata column and apply a two-
sided Mantel test to identify correlation between two distance matrices.
Actions used internally: `distance-matrix` from q2-metadata and `mantel`
from q2-diversity.
Inputs:
--i-distance-matrix ARTIFACT
DistanceMatrix Matrix of distances between pairs of samples.
[required]
Parameters:
--m-metadata-file METADATA
--m-metadata-column COLUMN MetadataColumn[Numeric]
Numeric metadata column from which to compute
pairwise Euclidean distances [required]
--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 `distance-matrix` in the output
visualization. [default: 'Distance Matrix']
--p-label2 TEXT Label for `metadata-distance-matrix` in the output
visualization. [default: 'Metadata']
Outputs:
--o-metadata-distance-matrix ARTIFACT
DistanceMatrix The Distance Matrix produced from the metadata
column and used in the mantel test [required]
--o-mantel-scatter-visualization VISUALIZATION
Scatter plot rendering of the manteltest results
[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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. 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.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.diversity.pipelines import beta_correlation
Docstring:
Beta diversity correlation
Create a distance matrix from a numeric metadata column and apply a two-
sided Mantel test to identify correlation between two distance matrices.
Actions used internally: `distance-matrix` from q2-metadata and `mantel`
from q2-diversity.
Parameters
----------
distance_matrix : DistanceMatrix
Matrix of distances between pairs of samples.
metadata : MetadataColumn[Numeric]
Numeric metadata column from which to compute pairwise Euclidean
distances
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 `distance_matrix` in the output visualization.
label2 : Str, optional
Label for `metadata_distance_matrix` in the output visualization.
Returns
-------
metadata_distance_matrix : DistanceMatrix
The Distance Matrix produced from the metadata column and used in the
mantel test
mantel_scatter_visualization : Visualization
Scatter plot rendering of the manteltest results
