micom.viz.exchanges
===================

.. py:module:: micom.viz.exchanges

.. autoapi-nested-parse::

   Visualization for exchanges.



Functions
---------

.. autoapisummary::

   micom.viz.exchanges.plot_exchanges_per_sample
   micom.viz.exchanges.plot_exchanges_per_taxon


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

.. py:function:: plot_exchanges_per_sample(results: micom.workflows.results.GrowthResults, filename: str = 'sample_exchanges_%s.html' % datetime.now().strftime('%Y%m%d'), direction: str = 'import', cluster: bool = True) -> None

   Plot the per sample exchange fluxes.

   :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 direction: The direction of fluxes to plot.
   :type direction: str either "import" or "export"
   :param cluster: Whether to reorder samples so that samples with similar exchange
                   fluxes are close to another.
   :type cluster: bool

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


.. py:function:: plot_exchanges_per_taxon(results: micom.workflows.results.GrowthResults, filename: str = 'taxon_exchanges_%s.html' % datetime.now().strftime('%Y%m%d'), direction: str = 'import', groups: pandas.Series = None, use_total_flux: bool = False, **tsne_args) -> None

   Plot the exchange fluxes per taxon.

   :param results: The exchanges 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 direction: The direction of fluxes to plot.
   :type direction: str either "import" or "export"
   :param groups: Additional metadata to color exchanges. 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 use_total_fluxes: Whether to use fluxes normalized to 1gDW of bacteria or the total flux.
   :type use_total_fluxes: bool
   :param tsne_args: Additional arguments passed to TSNE.
   :type tsne_args: dict

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