dfba.plot.plotly

Provide functions to plot concentrations and trajectories using plotly.

Module Contents

Functions

plot_concentrations(results: DataFrame, metabolites: Optional[List[str]] = None, biomass: str = ‘Biomass’, time: str = ‘time’, labels: Optional[Dict[str, str]] = None, x_axis_title: str = ‘$\textrm{Time} \left[ \textrm{h} \right]$’, left_y_axis_title: str = ‘$\textrm{Biomass} \left[ \textrm{g} \, \textrm{L}^{-1} \right]$’, right_y_axis_title: str = ‘$\textrm{Metabolites} \left[ \textrm{mmol} \, \textrm{L}^{-1} \right]$’) Plot the concentration results of a dynamic FBA simulation.
plot_trajectories(results: DataFrame, reactions: Optional[List[str]] = None, time: str = ‘time’, labels: Optional[Dict[str, str]] = None, x_axis_title: str = ‘$\textrm{Time} \left[ \textrm{h} \right]$’, y_axis_title: str = ‘$\textrm{Flux} \left[ \textrm{mmol} \, \textrm{g}_{\textrm{DW}}^{-1} \, \textrm{h}^{-1} \right]$’) Plot the flux trajectories of a dynamic FBA simulation.
dfba.plot.plotly.plot_concentrations(results: DataFrame, metabolites: Optional[List[str]] = None, biomass: str = 'Biomass', time: str = 'time', labels: Optional[Dict[str, str]] = None, x_axis_title: str = '$\textrm{Time} \left[ \textrm{h} \right]$', left_y_axis_title: str = '$\textrm{Biomass} \left[ \textrm{g} \, \textrm{L}^{-1} \right]$', right_y_axis_title: str = '$\textrm{Metabolites} \left[ \textrm{mmol} \, \textrm{L}^{-1} \right]$') → go.Figure[source]

Plot the concentration results of a dynamic FBA simulation.

The resulting plot can be further customized using the plotly backend.

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

2 y-axes: biomass on the left, (concentration / time)

metabolites on the right (concentration / time)

x-axis: time
Return type:

plotly.graph_objects.Figure
dfba.plot.plotly.plot_trajectories(results: DataFrame, reactions: Optional[List[str]] = None, time: str = 'time', labels: Optional[Dict[str, str]] = None, x_axis_title: str = '$\textrm{Time} \left[ \textrm{h} \right]$', y_axis_title: str = '$\textrm{Flux} \left[ \textrm{mmol} \, \textrm{g}_{\textrm{DW}}^{-1} \, \textrm{h}^{-1} \right]$') → go.Figure[source]

Plot the flux trajectories of a dynamic FBA simulation.

The resulting plot can be further customized using the plotly backend.

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

y-axis: flux trajectories (concentration / cell mass / time). x-axis: time
Return type:

plotly.graph_objects.Figure