amici.plotting

Plotting

Plotting related functions

Functions

plotObservableTrajectories(rdata[, ...])	Plot observable trajectories
plotStateTrajectories(rdata[, ...])	Plot state trajectories
plot_jacobian(rdata)	Plot Jacobian as heatmap.
plot_observable_trajectories(rdata[, ...])	Plot observable trajectories
plot_state_trajectories(rdata[, ...])	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 by amici.amici.runAmiciSimulation()

• observable_indices (typing.Optional[typing.Iterable[int]]) – Indices of observables for which trajectories are to be plotted

• ax (typing.Optional[matplotlib.axes._axes.Axes]) – matplotlib Axes instance to plot into

• model (typing.Optional[amici.amici.Model]) – amici model instance

• prefer_names (bool) – Whether observables names should be preferred over IDs, if available.

Return type

None

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 by amici.amici.runAmiciSimulation()

• state_indices (typing.Optional[typing.Iterable[int]]) – Indices of states for which trajectories are to be plotted

• ax (typing.Optional[matplotlib.axes._axes.Axes]) – matplotlib Axes instance to plot into

• model (typing.Optional[amici.amici.Model]) – amici model instance

• prefer_names (bool) – Whether state names should be preferred over IDs, if available.

Return type

None

amici.plotting.plot_jacobian(rdata)

Plot Jacobian as heatmap.

amici.plotting.plot_observable_trajectories(rdata, observable_indices=None, ax=None, model=None, prefer_names=True)

Plot observable trajectories

Parameters

• rdata (amici.numpy.ReturnDataView) – AMICI simulation results as returned by amici.amici.runAmiciSimulation()

• observable_indices (typing.Optional[typing.Iterable[int]]) – Indices of observables for which trajectories are to be plotted

• ax (typing.Optional[matplotlib.axes._axes.Axes]) – matplotlib Axes instance to plot into

• model (typing.Optional[amici.amici.Model]) – amici model instance

• prefer_names (bool) – Whether observables names should be preferred over IDs, if available.

Return type

None

amici.plotting.plot_state_trajectories(rdata, state_indices=None, ax=None, model=None, prefer_names=True)

Plot state trajectories

Parameters

• rdata (amici.numpy.ReturnDataView) – AMICI simulation results as returned by amici.amici.runAmiciSimulation()

• state_indices (typing.Optional[typing.Iterable[int]]) – Indices of states for which trajectories are to be plotted

• ax (typing.Optional[matplotlib.axes._axes.Axes]) – matplotlib Axes instance to plot into

• model (typing.Optional[amici.amici.Model]) – amici model instance

• prefer_names (bool) – Whether state names should be preferred over IDs, if available.

Return type

None