pypesto.visualize.model_fit
Visualization of the model fit after optimization.
Currently only for PEtab problems.
Functions
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Visualize the time trajectory of the model with given timepoints. |
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Visualize the optimized model fit of a PEtab problem. |
- pypesto.visualize.model_fit.time_trajectory_model(result, problem=None, timepoints=None, n_timepoints=1000, start_index=0, state_ids=None, state_names=None, observable_ids=None)[source]
Visualize the time trajectory of the model with given timepoints.
It does this by calling the amici plotting routines.
- Parameters:
result (
Union
[Result
,Sequence
[Result
]]) – The result object from optimization.problem (
Problem
) – A pypesto problem. Default is ‘None’ in which case result.problem is used. Needed in case the result is loaded from hdf5.timepoints (
Union
[ndarray
,Sequence
[ndarray
]]) – Array of timepoints, at which the trajectory will be plotted.n_timepoints (
int
) – Number of timepoints to be plotted between 0 and last measurement of the model. Only used when timepoints==None.start_index (
int
) – Index of Optimization run to be plotted. Default is best start.state_ids (
Union
[str
,Sequence
[str
]]) – Ids of the states to be plotted.state_names (
Union
[str
,Sequence
[str
]]) – Names of the states to be plotted.observable_ids (
Union
[str
,Sequence
[str
]]) – Ids of the observables to be plotted.
- Return type:
- Returns:
axes – matplotlib.axes.Axes object of the plot.
- pypesto.visualize.model_fit.visualize_optimized_model_fit(petab_problem, result, pypesto_problem, start_index=0, return_dict=False, unflattened_petab_problem=None, **kwargs)[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 (
Problem
) – Thepetab.Problem
that was optimized.result (
Union
[Result
,Sequence
[Result
]]) – The result object from optimization.start_index (
int
) – The index of the optimization run in result.optimize_result.list. Ignored if problem_parameters is provided.pypesto_problem (
Problem
) – The pyPESTO problem.return_dict (
bool
) – Return plot and simulation results as a dictionary.unflattened_petab_problem (
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()
.
- Return type:
- Returns:
axes (matplotlib.axes.Axes object of the created plot.)
None (In case subplots are saved to file)