petab.v1.visualize.plot_data_and_simulation
Functions for plotting PEtab measurement files and simulation results in the same format.
Functions
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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. |
- petab.v1.visualize.plot_data_and_simulation.plot_problem(petab_problem: Problem, simulations_df: str | DataFrame | None = None, grouping_list: list[list[str]] | None = None, group_by: str = 'observable', plotted_noise: str = 'MeanAndSD', subplot_dir: str | None = None, plotter_type: str = 'mpl') dict[str, Axes] | None [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.v1.visualize.plot_data_and_simulation.plot_with_vis_spec(vis_spec_df: str | DataFrame, conditions_df: str | DataFrame, measurements_df: str | DataFrame | None = None, simulations_df: str | DataFrame | None = None, subplot_dir: str | None = None, plotter_type: str = 'mpl', format_: str = 'png') dict[str, Axes] | None [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.v1.visualize.plot_data_and_simulation.plot_without_vis_spec(conditions_df: str | DataFrame, grouping_list: list[list[str]] | None = None, group_by: str = 'observable', measurements_df: str | DataFrame | None = None, simulations_df: str | DataFrame | None = None, plotted_noise: str = 'MeanAndSD', subplot_dir: str | None = None, plotter_type: str = 'mpl', format_: str = 'png') dict[str, Axes] | None [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.)