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core-features: Identify core features in table¶
Docstring:
Usage: qiime feature-table core-features [OPTIONS]
Identify "core" features, which are features observed in a user-defined
fraction of the samples. Since the core features are a function of the
fraction of samples that the feature must be observed in to be considered
core, this is computed over a range of fractions defined by the
`min_fraction`, `max_fraction`, and `steps` parameters.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
The feature table to use in core features
calculations. [required]
Parameters:
--p-min-fraction PROPORTION Range(0.0, 1.0, inclusive_start=False)
The minimum fraction of samples that a feature must
be observed in for that feature to be considered a
core feature. [default: 0.5]
--p-max-fraction PROPORTION Range(0.0, 1.0, inclusive_end=True)
The maximum fraction of samples that a feature must
be observed in for that feature to be considered a
core feature. [default: 1.0]
--p-steps INTEGER The number of steps to take between `min-fraction`
Range(2, None) and `max-fraction` for core features calculations.
This parameter has no effect if `min-fraction` and
`max-fraction` are the same value. [default: 11]
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.feature_table.visualizers import core_features
Docstring:
Identify core features in table
Identify "core" features, which are features observed in a user-defined
fraction of the samples. Since the core features are a function of the
fraction of samples that the feature must be observed in to be considered
core, this is computed over a range of fractions defined by the
`min_fraction`, `max_fraction`, and `steps` parameters.
Parameters
----------
table : FeatureTable[Frequency]
The feature table to use in core features calculations.
min_fraction : Float % Range(0.0, 1.0, inclusive_start=False), optional
The minimum fraction of samples that a feature must be observed in for
that feature to be considered a core feature.
max_fraction : Float % Range(0.0, 1.0, inclusive_end=True), optional
The maximum fraction of samples that a feature must be observed in for
that feature to be considered a core feature.
steps : Int % Range(2, None), optional
The number of steps to take between `min_fraction` and `max_fraction`
for core features calculations. This parameter has no effect if
`min_fraction` and `max_fraction` are the same value.
Returns
-------
visualization : Visualization