petab.visualize.plot_data_and_simulation

Functions for plotting PEtab measurement files and simulation results in the same format.

Functions

plot_problem(petab_problem[, ...])

Visualization using petab problem.

plot_with_vis_spec(vis_spec_df, conditions_df)

Plot measurements and/or simulations.

plot_without_vis_spec(conditions_df[, ...])

Plot measurements and/or simulations.
petab.visualize.plot_data_and_simulation.plot_problem(petab_problem: Problem, simulations_df: Optional[Union[str, DataFrame]] = None, grouping_list: Optional[List[List[str]]] = None, group_by: str = 'observable', plotted_noise: str = 'MeanAndSD', subplot_dir: Optional[str] = None, plotter_type: str = 'mpl') → Optional[Dict[str, Axes]][source]

Visualization using petab problem. If Visualization table is part of the petab_problem, it will be used for visualization. Otherwise, grouping_list will be used. If neither Visualization table nor grouping_list are available, measurements (simulations) will be grouped by observable, i.e. all measurements for each observable will be visualized on one plot.

Parameters:

  • petab_problem – A PEtab problem.

  • simulations_df – A simulation DataFrame in the PEtab format or path to the simulation output data file.

  • grouping_list – A list of lists. Each sublist corresponds to a plot, each subplot contains the Ids of datasets or observables or simulation conditions for this plot.

  • group_by – Possible values: ‘dataset’, ‘observable’, ‘simulation’.

  • plotted_noise – A string indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’].

  • subplot_dir – A string which is taken as path to the folder where single subplots should be saved. PlotIDs will be taken as file names.

  • plotter_type – Specifies which library should be used for plot generation. Currently, only matplotlib is supported.

Returns:

  • ax (Axis object of the created plot.)

  • None (In case subplots are saved to a file.)

petab.visualize.plot_data_and_simulation.plot_with_vis_spec(vis_spec_df: Union[str, DataFrame], conditions_df: Union[str, DataFrame], measurements_df: Optional[Union[str, DataFrame]] = None, simulations_df: Optional[Union[str, DataFrame]] = None, subplot_dir: Optional[str] = None, plotter_type: str = 'mpl', format_: str = 'png') → Optional[Dict[str, Axes]][source]

Plot measurements and/or simulations. Specification of the visualization routines is provided in visualization table.

Parameters:

  • vis_spec_df – A visualization table.

  • conditions_df – A condition DataFrame in the PEtab format or path to the condition file.

  • measurements_df – A measurement DataFrame in the PEtab format or path to the data file.

  • simulations_df – A simulation DataFrame in the PEtab format or path to the simulation output data file.

  • subplot_dir – A path to the folder where single subplots should be saved. PlotIDs will be taken as file names.

  • plotter_type – Specifies which library should be used for plot generation. Currently, only matplotlib is supported.

  • format – File format for the generated figure. (See matplotlib.pyplot.savefig() for supported options).

Returns:

  • ax (Axis object of the created plot.)

  • None (In case subplots are saved to a file.)

petab.visualize.plot_data_and_simulation.plot_without_vis_spec(conditions_df: Union[str, DataFrame], grouping_list: Optional[List[List[str]]] = None, group_by: str = 'observable', measurements_df: Optional[Union[str, DataFrame]] = None, simulations_df: Optional[Union[str, DataFrame]] = None, plotted_noise: str = 'MeanAndSD', subplot_dir: Optional[str] = None, plotter_type: str = 'mpl', format_: str = 'png') → Optional[Dict[str, Axes]][source]

Plot measurements and/or simulations. What exactly should be plotted is specified in a grouping_list. If grouping list is not provided, measurements (simulations) will be grouped by observable, i.e. all measurements for each observable will be visualized on one plot.

Parameters:

  • grouping_list – A list of lists. Each sublist corresponds to a plot, each subplot contains the Ids of datasets or observables or simulation conditions for this plot.

  • group_by – Grouping type. Possible values: ‘dataset’, ‘observable’, ‘simulation’.

  • conditions_df – A condition DataFrame in the PEtab format or path to the condition file.

  • measurements_df – A measurement DataFrame in the PEtab format or path to the data file.

  • simulations_df – A simulation DataFrame in the PEtab format or path to the simulation output data file.

  • plotted_noise – A string indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’].

  • subplot_dir – A path to the folder where single subplots should be saved. PlotIDs will be taken as file names.

  • plotter_type – Specifies which library should be used for plot generation. Currently, only matplotlib is supported.

  • format – File format for the generated figure. (See matplotlib.pyplot.savefig() for supported options).

Returns:

  • ax (Axis object of the created plot.)

  • None (In case subplots are saved to a file.)