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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  The feature table to use in core features
                                  calculations.  [required]
  --p-min-fraction FLOAT          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 FLOAT          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 RANGE         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.  [default: 11]
  --o-visualization VISUALIZATION PATH
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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