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core-features: Identify core features in tableΒΆ

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` and
    Range(2, None)     `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).
  --citations          Show citations and exit.
  --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