amici.plotting
Plotting
Plotting related functions
Functions
|
Plot observable trajectories |
|
Plot state trajectories |
|
Plot the given expressions evaluated on the given simulation outputs. |
|
Plot Jacobian as heatmap. |
|
Plot observable trajectories |
|
Plot state trajectories |
- amici.plotting.plotObservableTrajectories(rdata, observable_indices=None, ax=None, model=None, prefer_names=True)
Plot observable trajectories
- Parameters
rdata (
amici.numpy.ReturnDataView
) – AMICI simulation results as returned byamici.amici.runAmiciSimulation()
observable_indices (
typing.Optional
[typing.Iterable
[int
]]) – Indices of observables for which trajectories are to be plottedax (
typing.Optional
[matplotlib.axes._axes.Axes
]) – matplotlib Axes instance to plot intomodel (
typing.Optional
[amici.amici.Model
]) – amici model instanceprefer_names (
bool
) – Whether observables names should be preferred over IDs, if available.
- Return type
- amici.plotting.plotStateTrajectories(rdata, state_indices=None, ax=None, model=None, prefer_names=True)
Plot state trajectories
- Parameters
rdata (
amici.numpy.ReturnDataView
) – AMICI simulation results as returned byamici.amici.runAmiciSimulation()
state_indices (
typing.Optional
[typing.Iterable
[int
]]) – Indices of states for which trajectories are to be plottedax (
typing.Optional
[matplotlib.axes._axes.Axes
]) – matplotlib Axes instance to plot intomodel (
typing.Optional
[amici.amici.Model
]) – amici model instanceprefer_names (
bool
) – Whether state names should be preferred over IDs, if available.
- Return type
- amici.plotting.plot_expressions(exprs, rdata)[source]
Plot the given expressions evaluated on the given simulation outputs.
- Parameters
exprs (
typing.Union
[typing.Sequence
[typing.Union
[str
,sympy.core.expr.Expr
]],str
,sympy.core.expr.Expr
]) – A symbolic expression, e.g. a sympy expression or a string that can be sympified. Can include state variable, expression, and observable IDs, depending on whether the respective data is available in the simulation results. Parameters are not yet supported.rdata (
amici.numpy.ReturnDataView
) – The simulation results.
- Return type
- amici.plotting.plot_observable_trajectories(rdata, observable_indices=None, ax=None, model=None, prefer_names=True)[source]
Plot observable trajectories
- Parameters
rdata (
amici.numpy.ReturnDataView
) – AMICI simulation results as returned byamici.amici.runAmiciSimulation()
observable_indices (
typing.Optional
[typing.Iterable
[int
]]) – Indices of observables for which trajectories are to be plottedax (
typing.Optional
[matplotlib.axes._axes.Axes
]) – matplotlib Axes instance to plot intomodel (
typing.Optional
[amici.amici.Model
]) – amici model instanceprefer_names (
bool
) – Whether observables names should be preferred over IDs, if available.
- Return type
- amici.plotting.plot_state_trajectories(rdata, state_indices=None, ax=None, model=None, prefer_names=True)[source]
Plot state trajectories
- Parameters
rdata (
amici.numpy.ReturnDataView
) – AMICI simulation results as returned byamici.amici.runAmiciSimulation()
state_indices (
typing.Optional
[typing.Iterable
[int
]]) – Indices of states for which trajectories are to be plottedax (
typing.Optional
[matplotlib.axes._axes.Axes
]) – matplotlib Axes instance to plot intomodel (
typing.Optional
[amici.amici.Model
]) – amici model instanceprefer_names (
bool
) – Whether state names should be preferred over IDs, if available.
- Return type