micom.viz.growth
================

.. py:module:: micom.viz.growth

.. autoapi-nested-parse::

   Visualization for growth rates.



Functions
---------

.. autoapisummary::

   micom.viz.growth.plot_growth


Module Contents
---------------

.. py:function:: plot_growth(results: micom.workflows.results.GrowthResults, filename: str = 'growth_rates_%s.html' % datetime.now().strftime('%Y%m%d'), groups: pandas.Series = None, tolerance: float = 1e-06) -> None

   Plot the taxa growth rates.

   :param results: The results returned by the `grow` workflow.
   :type results: micom.workflows.GrowthResults
   :param filename: The HTML file where the visualization will be saved.
   :type filename: str
   :param groups: Additional metadata to color points. The index must correspond to the
                  `sample_id` in the results and values must be categorical. The `.name` attribute
                  will be used to name the groups. If not provided will color by taxon.
   :type groups: pandas.Series
   :param tolerance: Smallest growth rate that will be considered. Everything lower will be
                     considered not growing.
   :type tolerance: float

   :returns: A MICOM visualization. Can be served with `viz.serve`.
   :rtype: Visualization