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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.

Inputs:
  --i-table ARTIFACT FeatureTable[RelativeFrequency]
                         Feature table containing features found in
                         importances.                               [required]
  --i-importances ARTIFACT FeatureData[Importance]
                         Feature importance scores.                 [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple            Sample metadata file containing
     arguments will be   individual-id-column.
     merged)                                                        [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 TEXT Choices('linear', 'pow', 'sqrt', 'log')
                         y-axis scaling strategy to apply. [default: 'linear']
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.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', 'pow', 'sqrt', 'log'), optional
    y-axis scaling strategy to apply.

Returns
-------
visualization : Visualization