petab.visualize.plot_data_and_simulation
Functions for plotting PEtab measurement files and simulation results in the same format.
Functions
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Main function for plotting data and simulations. |
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plot measurement data grouped by observable ID. |
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Visualization using petab problem. |
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Visualization using petab problem. |
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Plot measurements and/or simulations. |
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Plot measurements and/or simulations. |
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Generate and save visualization specification to a file. |
- petab.visualize.plot_data_and_simulation.plot_data_and_simulation(exp_data: Union[str, pandas.core.frame.DataFrame], exp_conditions: Union[str, pandas.core.frame.DataFrame], vis_spec: Optional[Union[str, pandas.core.frame.DataFrame]] = None, sim_data: Optional[Union[str, pandas.core.frame.DataFrame]] = None, dataset_id_list: Optional[List[List[str]]] = None, sim_cond_id_list: Optional[List[List[str]]] = None, sim_cond_num_list: Optional[List[List[int]]] = None, observable_id_list: Optional[List[List[str]]] = None, observable_num_list: Optional[List[List[int]]] = None, plotted_noise: Optional[str] = 'MeanAndSD', subplot_file_path: str = '') Optional[Union[Dict[str, matplotlib.axes._subplots.AxesSubplot], np.ndarray[plt.Subplot]]] [source]
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
exp_data – measurement DataFrame in the PEtab format or path to the data file.
exp_conditions – condition DataFrame in the PEtab format or path to the condition file.
vis_spec – Visualization specification DataFrame in the PEtab format or path to visualization file.
sim_data – simulation DataFrame in the PEtab format or path to the simulation output data file.
dataset_id_list – 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 – 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 – 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 – 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 – 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 – String indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’]
subplot_file_path – String which is taken as file path to which single subplots are saved. PlotIDs will be taken as file names.
- Returns
ax (Axis object of the created plot.)
None (In case subplots are save to file)
- petab.visualize.plot_data_and_simulation.plot_measurements_by_observable(data_file_path: str, condition_file_path: str, plotted_noise: Optional[str] = 'MeanAndSD') Optional[Union[Dict[str, matplotlib.axes._subplots.AxesSubplot], np.ndarray[plt.Subplot]]] [source]
plot measurement data grouped by observable ID. A simple wrapper around the more complex function plot_data_and_simulation.
- Parameters
data_file_path – file path of measurement data
condition_file_path – file path of condition file
plotted_noise – String indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’]
- Returns
ax
- Return type
axis of figures
- petab.visualize.plot_data_and_simulation.plot_petab_problem(petab_problem: petab.problem.Problem, sim_data: Optional[Union[str, pandas.core.frame.DataFrame]] = None, dataset_id_list: Optional[List[List[str]]] = None, sim_cond_id_list: Optional[List[List[str]]] = None, sim_cond_num_list: Optional[List[List[int]]] = None, observable_id_list: Optional[List[List[str]]] = None, observable_num_list: Optional[List[List[int]]] = None, plotted_noise: Optional[str] = 'MeanAndSD') Optional[Union[Dict[str, matplotlib.axes._subplots.AxesSubplot], np.ndarray[plt.Subplot]]] [source]
Visualization using petab problem. For documentation, see function plot_data_and_simulation()
- petab.visualize.plot_data_and_simulation.plot_problem(petab_problem: petab.problem.Problem, simulations_df: Optional[Union[str, pandas.core.frame.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, matplotlib.axes._subplots.AxesSubplot]] [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, conditions_df: Union[str, pandas.core.frame.DataFrame], measurements_df: Optional[Union[str, pandas.core.frame.DataFrame]] = None, simulations_df: Optional[Union[str, pandas.core.frame.DataFrame]] = None, subplot_dir: Optional[str] = None, plotter_type: str = 'mpl') Optional[Dict[str, matplotlib.axes._subplots.AxesSubplot]] [source]
Plot measurements and/or simulations. Specification of the visualization routines is provided in visualization table.
- Parameters
vis_spec_df (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.
- 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, pandas.core.frame.DataFrame], grouping_list: Optional[List[List[str]]] = None, group_by: str = 'observable', measurements_df: Optional[Union[str, pandas.core.frame.DataFrame]] = None, simulations_df: Optional[Union[str, pandas.core.frame.DataFrame]] = None, plotted_noise: str = 'MeanAndSD', subplot_dir: Optional[str] = None, plotter_type: str = 'mpl') Optional[Dict[str, matplotlib.axes._subplots.AxesSubplot]] [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
- Returns
ax (Axis object of the created plot.)
None (In case subplots are saved to a file.)
- petab.visualize.plot_data_and_simulation.save_vis_spec(exp_data: Union[str, pandas.core.frame.DataFrame], exp_conditions: Union[str, pandas.core.frame.DataFrame], vis_spec: Optional[Union[str, pandas.core.frame.DataFrame]] = None, dataset_id_list: Optional[List[List[str]]] = None, sim_cond_id_list: Optional[List[List[str]]] = None, sim_cond_num_list: Optional[List[List[int]]] = None, observable_id_list: Optional[List[List[str]]] = None, observable_num_list: Optional[List[List[int]]] = None, plotted_noise: Optional[str] = 'MeanAndSD', output_file_path: str = 'visuSpec.tsv')[source]
Generate and save visualization specification to a file. If vis_spec is provided, the missing columns will be added.
- Parameters
exp_data – Measurement DataFrame in the PEtab format or path to the data file.
exp_conditions – Condition DataFrame in the PEtab format or path to the condition file.
vis_spec – Visualization specification DataFrame in the PEtab format or path to visualization file.
dataset_id_list – 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 – 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 – 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 – 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 – 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 – String indicating how noise should be visualized: [‘MeanAndSD’ (default), ‘MeanAndSEM’, ‘replicate’, ‘provided’]
output_file_path – File path to which the generated visualization specification is saved.