`dfba.plot.plotly`¶

Provide functions to plot concentrations and trajectories using plotly.

Module Contents¶

Functions¶

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 = '$\\textrm{Time} \\left[ \\textrm{h} \\right]$', left_y_axis_title: str = '$\\textrm{Biomass} \\left[ \\textrm{g} \\, \\textrm{L}^{-1} \\right]$', right_y_axis_title: str = '$\\textrm{Metabolites} \\left[ \\textrm{mmol} \\, \\textrm{L}^{-1} \\right]$') → plotly.graph_objects.Figure

Plot the concentration results of a dynamic FBA simulation.

plot_trajectories(results: pandas.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 = '$\\textrm{Flux} \\left[ \\textrm{mmol} \\, \\textrm{g}_{\\textrm{DW}}^{-1} \\, \\textrm{h}^{-1} \\right]$') → plotly.graph_objects.Figure

Plot the flux trajectories of a dynamic FBA simulation.

dfba.plot.plotly.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 = '$\\textrm{Time} \\left[ \\textrm{h} \\right]$', left_y_axis_title: str = '$\\textrm{Biomass} \\left[ \\textrm{g} \\, \\textrm{L}^{-1} \\right]$', right_y_axis_title: str = '$\\textrm{Metabolites} \\left[ \\textrm{mmol} \\, \\textrm{L}^{-1} \\right]$') → plotly.graph_objects.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: pandas.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 = '$\\textrm{Flux} \\left[ \\textrm{mmol} \\, \\textrm{g}_{\\textrm{DW}}^{-1} \\, \\textrm{h}^{-1} \\right]$') → plotly.graph_objects.Figure[source]¶