:mod:`dfba.plot.matplotlib`
===========================

.. py:module:: dfba.plot.matplotlib

.. autoapi-nested-parse::

   Provide functions to plot concentrations and trajectories using pyplot.



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


Functions
~~~~~~~~~

.. autoapisummary::

   dfba.plot.matplotlib.plot_concentrations
   dfba.plot.matplotlib.plot_trajectories



Attributes
~~~~~~~~~~

.. autoapisummary::

   dfba.plot.matplotlib.PALETTE


.. data:: PALETTE
   :annotation: = ['#ff7f00', '#32ff00', '#19b2ff', '#654cff', '#e51932', '#000000', '#ffff32', '#ff99bf',...

   

.. function:: plot_concentrations(results: pandas.DataFrame, metabolites: Optional[List[str]] = None, biomass: str = 'Biomass', time: str = 'time', labels: Optional[Dict[str, str]] = None, x_axis_title: str = 'Time $\\left[ \\mathrm{h} \\right]$', left_y_axis_title: str = 'Biomass $\\left[ \\mathrm{g} \\, \\mathrm{L}^{-1} \\right]$', right_y_axis_title: str = 'Metabolites $\\left[ \\mathrm{mmol} \\, \\mathrm{L}^{-1} \\right]$') -> None

   Plot the concentration results of a dynamic FBA simulation.

   The resulting plot can be further customized using ``matplotlib.pyplot``.

   :param results: The concentration results of a simulation.
   :type results: pandas.DataFrame
   :param metabolites: The names of the metabolites in the data frame (default: all columns
                       except for time and biomass).
   :type metabolites: list of strings, optional
   :param biomass: The name of biomass in the results (default "Biomass").
   :type biomass: str, optional
   :param time: The name of the time column in the results (default "time").
   :type time: str, optional
   :param labels: A mapping from columns names to legend labels (default is the same).
   :type labels: dict, optional
   :param x_axis_title: The axis title for the horizontal axis (default time).
   :type x_axis_title: str, optional
   :param left_y_axis_title: The left vertical axis title (default biomass).
   :type left_y_axis_title: str, optional
   :param right_y_axis_title: The right vertical axis title (default metabolite concentration).
   :type right_y_axis_title: str, optional


.. function:: plot_trajectories(results: pandas.DataFrame, reactions: Optional[List[str]] = None, time: str = 'time', labels: Optional[Dict[str, str]] = None, x_axis_title: str = 'Time $\\left[ \\mathrm{h} \\right]$', y_axis_title: str = 'Flux $\\left[ \\mathrm{mmol} \\, \\mathrm{g}_{\\mathrm{DW}}^{-1} \\, \\mathrm{h}^{-1} \\right]$') -> None

   Plot the flux trajectories of a dynamic FBA simulation.

   The resulting plot can be further customized using ``matplotlib.pyplot``.

   :param results: The flux results of a simulation.
   :type results: pandas.DataFrame
   :param reactions: The names of the reactions in the data frame (default: all columns
                     except for time).
   :type reactions: list of strings, optional
   :param time: The name of the time column in the results (default "time").
   :type time: str, optional
   :param labels: A mapping from columns names to legend labels (default is the same).
   :type labels: dict, optional
   :param x_axis_title: The axis title for the horizontal axis (default time).
   :type x_axis_title: str, optional
   :param y_axis_title: The vertical axis title (default flux).
                        x-axis: time
   :type y_axis_title: str, optional