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volatility: Generate interactive volatility plotΒΆ

Docstring:

Usage: qiime longitudinal volatility [OPTIONS]

  Generate an interactive control chart depicting the longitudinal
  volatility of sample metadata and/or feature frequencies across time (as
  set using the "state_column" parameter). Any numeric metadata column (and
  metadata-transformable artifacts, e.g., alpha diversity results) can be
  plotted on the y-axis, and are selectable using the "metric_column"
  selector. Metric values are averaged to compare across any categorical
  metadata column using the "group_column" selector. Longitudinal volatility
  for individual subjects sampled over time is co-plotted as "spaghetti"
  plots if the "individual_id_column" parameter is used. state_column will
  typically be a measure of time, but any numeric metadata column can be
  used.

Options:
  --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-default-metric TEXT         Numeric metadata or artifact column to test
                                  by default (all numeric metadata columns
                                  will be available in the visualization).
                                  [optional]
  --i-table ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  Feature table containing metrics.
                                  [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 volatility

Docstring:

Generate interactive volatility plot

Generate an interactive control chart depicting the longitudinal volatility
of sample metadata and/or feature frequencies across time (as set using the
"state_column" parameter). Any numeric metadata column (and metadata-
transformable artifacts, e.g., alpha diversity results) can be plotted on
the y-axis, and are selectable using the "metric_column" selector. Metric
values are averaged to compare across any categorical metadata column using
the "group_column" selector. Longitudinal volatility for individual
subjects sampled over time is co-plotted as "spaghetti" plots if the
"individual_id_column" parameter is used. state_column will typically be a
measure of time, but any numeric metadata column can be used.

Parameters
----------
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).
default_metric : Str, optional
    Numeric metadata or artifact column to test by default (all numeric
    metadata columns will be available in the visualization).
table : FeatureTable[RelativeFrequency], optional
    Feature table containing metrics.
yscale : Str % Choices({'linear', 'log', 'pow', 'sqrt'}), optional
    y-axis scaling strategy to apply.

Returns
-------
visualization : Visualization