amici.plotting

Plotting

Plotting related functions

Functions

plotObservableTrajectories(rdata[, ...])	Plot observable trajectories.
plotStateTrajectories(rdata[, ...])	Plot state trajectories.
plot_expressions(exprs, rdata)	Plot the given expressions evaluated on the given simulation outputs.
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, marker=None, edata=None)

Plot observable trajectories.

Parameters:

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

• observable_indices (collections.abc.Iterable[int] | None) – Indices of observables for which trajectories are to be plotted.

• ax (matplotlib.axes._axes.Axes | None) – matplotlib.pyplot.Axes instance to plot into.

• model (amici.amici.Model) – The model rdata was generated from.

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

• marker – Point marker for plotting (see matplotlib documentation).

• edata (amici.amici.ExpData | amici.numpy.ExpDataView) – Experimental data to be plotted (no event observables yet).

Return type:

None

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

Plot state trajectories.

Parameters:

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

• state_indices (collections.abc.Sequence[int] | None) – Indices of state variables for which trajectories are to be plotted.

• ax (matplotlib.axes._axes.Axes | None) – matplotlib.pyplot.Axes instance to plot into.

• model (amici.amici.Model) – The model rdata was generated from.

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

• marker –

  Point marker for plotting (see matplotlib documentation).

Return type:

None

amici.plotting.plot_expressions(exprs, rdata)

Plot the given expressions evaluated on the given simulation outputs.

Parameters:

• exprs (collections.abc.Sequence[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. It 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:

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, marker=None, edata=None)

Plot observable trajectories.

Parameters:

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

• observable_indices (collections.abc.Iterable[int] | None) – Indices of observables for which trajectories are to be plotted.

• ax (matplotlib.axes._axes.Axes | None) – matplotlib.pyplot.Axes instance to plot into.

• model (amici.amici.Model) – The model rdata was generated from.

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

• marker –

  Point marker for plotting (see matplotlib documentation).

• edata (amici.amici.ExpData | amici.numpy.ExpDataView) – Experimental data to be plotted (no event observables yet).

Return type:

None

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

Plot state trajectories.

Parameters:

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

• state_indices (collections.abc.Sequence[int] | None) – Indices of state variables for which trajectories are to be plotted.

• ax (matplotlib.axes._axes.Axes | None) – matplotlib.pyplot.Axes instance to plot into.

• model (amici.amici.Model) – The model rdata was generated from.

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

• marker –

  Point marker for plotting (see matplotlib documentation).

Return type:

None