pypesto.visualize.model_fit
Visualization of the model fit after optimization.
Currently only for PEtab problems.
Functions
|
Visualize the time trajectory of the model with given timepoints. |
|
Visualize the optimized model fit of a PEtab problem. |
- pypesto.visualize.model_fit.time_trajectory_model(result: Result | Sequence[Result], problem: Problem | None = None, timepoints: ndarray | Sequence[ndarray] | None = None, n_timepoints: int = 1000, start_index: int = 0, state_ids: str | Sequence[str] | None = None, state_names: str | Sequence[str] | None = None, observable_ids: str | Sequence[str] | None = None) Axes | None [source]
Visualize the time trajectory of the model with given timepoints.
It does this by calling the amici plotting routines.
- Parameters:
result – The result object from optimization.
problem – A pypesto problem. Default is ‘None’ in which case result.problem is used. Needed in case the result is loaded from hdf5.
timepoints – Array of timepoints, at which the trajectory will be plotted.
n_timepoints – Number of timepoints to be plotted between 0 and last measurement of the model. Only used when timepoints==None.
start_index – Index of Optimization run to be plotted. Default is best start.
state_ids – Ids of the states to be plotted.
state_names – Names of the states to be plotted.
observable_ids – Ids of the observables to be plotted.
- Returns:
matplotlib.axes.Axes object of the plot.
- Return type:
axes
- pypesto.visualize.model_fit.visualize_optimized_model_fit(petab_problem: Problem, result: Result | Sequence[Result], pypesto_problem: Problem, start_index: int = 0, return_dict: bool = False, unflattened_petab_problem: Problem | None = None, **kwargs) Axes | None [source]
Visualize the optimized model fit of a PEtab problem.
Function calls the PEtab visualization file of the
petab_problem
and visualizes the fit of the optimized parameter. Common additional argument issubplot_dir
to specify the directory each subplot is saved to. Further keyword arguments are delegated topetab.visualize.plot_with_vis_spec()
, see there for more information.- Parameters:
petab_problem – The
petab.Problem
that was optimized.result – The result object from optimization.
start_index – The index of the optimization run in result.optimize_result.list. Ignored if problem_parameters is provided.
pypesto_problem – The pyPESTO problem.
return_dict – Return plot and simulation results as a dictionary.
unflattened_petab_problem – If the original PEtab problem is flattened, this can be passed to plot with the original unflattened problem.
kwargs – Passed to
petab.visualize.plot_problem()
.
- Returns:
axes (matplotlib.axes.Axes object of the created plot.)
None (In case subplots are saved to file)