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plot-feature-volatility: Plot longitudinal feature volatility and importancesΒΆ

Docstring:

Usage: qiime longitudinal plot-feature-volatility [OPTIONS]

  Plots an interactive control chart of feature abundances (y-axis) in each
  sample across time (or state; x-axis). Feature importance scores and
  descriptive statistics for each each feature are plotted in interactive
  bar charts below the control chart, facilitating exploration of
  longitudinal feature data. This visualization is intended for use with the
  feature-volatility pipeline; use that pipeline to access this
  visualization.

Options:
  --i-table ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  Feature table containing features found in
                                  importances.  [required]
  --i-importances ARTIFACT PATH FeatureData[Importance]
                                  Feature importance scores.  [required]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata. Sample
                                  metadata file containing
                                  individual_id_column.  [required]
  --p-state-column TEXT           Metadata column containing state (time)
                                  variable information.  [required]
  --p-individual-id-column TEXT   Metadata column containing IDs for
                                  individual subjects.  [optional]
  --p-default-group-column TEXT   The default metadata column on which to
                                  separate groups for comparison (all
                                  categorical metadata columns will be
                                  available in the visualization).  [optional]
  --p-yscale [linear|log|sqrt|pow]
                                  y-axis scaling strategy to apply.  [default:
                                  linear]
  --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.longitudinal.visualizers import plot_feature_volatility

Docstring:

Plot longitudinal feature volatility and importances

Plots an interactive control chart of feature abundances (y-axis) in each
sample across time (or state; x-axis). Feature importance scores and
descriptive statistics for each each feature are plotted in interactive bar
charts below the control chart, facilitating exploration of longitudinal
feature data. This visualization is intended for use with the feature-
volatility pipeline; use that pipeline to access this visualization.

Parameters
----------
table : FeatureTable[RelativeFrequency]
    Feature table containing features found in importances.
importances : FeatureData[Importance]
    Feature importance scores.
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (time) variable information.
individual_id_column : Str, optional
    Metadata column containing IDs for individual subjects.
default_group_column : Str, optional
    The default metadata column on which to separate groups for comparison
    (all categorical metadata columns will be available in the
    visualization).
yscale : Str % Choices({'linear', 'log', 'pow', 'sqrt'}), optional
    y-axis scaling strategy to apply.

Returns
-------
visualization : Visualization