Docstring:
Usage: qiime diversity-lib shannon-entropy [OPTIONS]
Compute Shannon's Entropy for each sample in a feature table
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency]
The feature table containing the samples for which
Shannon's Entropy should be computed. [required]
Parameters:
--p-drop-undefined-samples / --p-no-drop-undefined-samples
Samples with no observed features produce undefined
(NaN) values. If true, these samples are dropped from
the output vector. [default: False]
Outputs:
--o-vector ARTIFACT SampleData[AlphaDiversity]
Vector containing per-sample values for Shannon's
Entropy. [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: basic
qiime diversity-lib shannon-entropy \
--i-table feature-table.qza \
--o-vector shannon-vector.qza
# ### example: dropping undefined samples
qiime diversity-lib shannon-entropy \
--i-table feature-table.qza \
--p-drop-undefined-samples \
--o-vector shannon-vector.qza
Import:
from qiime2.plugins.diversity_lib.methods import shannon_entropy
Docstring:
Shannon's Entropy
Compute Shannon's Entropy for each sample in a feature table
Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency]
The feature table containing the samples for which Shannon's Entropy
should be computed.
drop_undefined_samples : Bool, optional
Samples with no observed features produce undefined (NaN) values. If
true, these samples are dropped from the output vector.
Returns
-------
vector : SampleData[AlphaDiversity]
Vector containing per-sample values for Shannon's Entropy.
