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alpha-correlation: Alpha diversity correlation¶
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Docstring:
Usage: qiime diversity alpha-correlation [OPTIONS]
Determine whether numeric sample metadata columns are correlated with alpha
diversity.
Inputs:
--i-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
Vector of alpha diversity values by sample.
[required]
Parameters:
--m-metadata-file METADATA...
(multiple The sample metadata.
arguments will be
merged) [required]
--p-method TEXT Choices('spearman', 'pearson')
The correlation test to be applied.
[default: 'spearman']
--p-intersect-ids / --p-no-intersect-ids
If supplied, IDs that are not found in both the
alpha diversity vector and metadata will be discarded
before calculating the correlation. Default behavior
is to error on any mismatched IDs. [default: False]
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.
Examples:
# ### example: alpha correlation faith pd
qiime diversity alpha-correlation \
--i-alpha-diversity alpha-div-faith-pd.qza \
--m-metadata-file metadata.tsv \
--o-visualization visualization.qzv
Import:
from qiime2.plugins.diversity.visualizers import alpha_correlation
Docstring:
Alpha diversity correlation
Determine whether numeric sample metadata columns are correlated with alpha
diversity.
Parameters
----------
alpha_diversity : SampleData[AlphaDiversity]
Vector of alpha diversity values by sample.
metadata : Metadata
The sample metadata.
method : Str % Choices('spearman', 'pearson'), optional
The correlation test to be applied.
intersect_ids : Bool, optional
If supplied, IDs that are not found in both the alpha diversity vector
and metadata will be discarded before calculating the correlation.
Default behavior is to error on any mismatched IDs.
Returns
-------
visualization : Visualization