petab.visualize.plot_data_and_simulation

petab.visualize.plot_data_and_simulation(data_file_path: str, condition_file_path: str, visualization_file_path: str = '', simulation_file_path: str = '', dataset_id_list=None, sim_cond_id_list=None, sim_cond_num_list=None, observable_id_list=None, observable_num_list=None, plotted_noise: str = 'MeanAndSD')

Main function for plotting data and simulations.

What exactly should be plotted is specified in a visualizationSpecification.tsv file.

Also, the data, simulations and conditions have to be defined in a specific format (see “doc/documentation_data_format.md”).

Parameters:
  • data_file_path (str) – Path to the data file.
  • condition_file_path (str) – Path to the condition file.
  • visualization_file_path (str (optional)) – Path to the visualization specification file.
  • simulation_file_path (str (optional)) – Path to the simulation output data file.
  • dataset_id_list (list (optional)) – A list of lists. Each sublist corresponds to a plot, each subplot contains the datasetIds for this plot. Only to be used if no visualization file was available.
  • sim_cond_id_list (list (optional)) – A list of lists. Each sublist corresponds to a plot, each subplot contains the simulationConditionIds for this plot. Only to be used if no visualization file was available.
  • sim_cond_num_list (list (optional)) – A list of lists. Each sublist corresponds to a plot, each subplot contains the numbers corresponding to the simulationConditionIds for this plot. Only to be used if no visualization file was available.
  • observable_id_list (list (optional)) – A list of lists. Each sublist corresponds to a plot, each subplot contains the observableIds for this plot. Only to be used if no visualization file was available.
  • observable_num_list (list (optional)) – A list of lists. Each sublist corresponds to a plot, each subplot contains the numbers corresponding to the observableIds for this plot. Only to be used if no visualization file was available.
  • plotted_noise (str (optional)) – String indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’]
Returns:

ax

Return type:

Axis object of the created plot.