petab.visualize.plot_data_and_simulation¶
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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.