sbiosubplot

Plot simulation results in subplots

Syntax

sbiosubplot(sd)

sbiosubplot(sd,fcnHandle,xArgs,yArgs)

sbiosubplot(sd,fcnHandle,xArgs,yArgs,showLegend)

sbiosubplot(sd,fcnHandle,xArgs,yArgs,showLegend,Name,Value)

Description

sbiosubplot(sd) plots each simulation run from sd, a SimData object or array of objects, into its own subplot. The subplot is a time plot of each state in sd.

sbiosubplot(sd,fcnHandle,xArgs,yArgs) plots simulation results by calling the function handle fcnHandle with inputs sd, xArgs, and yArgs. The inputs xArgs and yArgs must be cell arrays of the names of the states to plot.

sbiosubplot(sd,fcnHandle,xArgs,yArgs,showLegend) also specifies whether to show the legend in the plot. If true, the function shows yArgs as the legend.

sbiosubplot(sd,fcnHandle,xArgs,yArgs,showLegend,Name,Value) also uses additional options specified by one or more name-value pair arguments. For example, you can specify the x-label and y-label of the plot.

Examples

Plot Selected States from Simulation Data in Subplots

Plot the prey versus predator data from the stochastically simulated lotka model in separate subplots by using a custom function (plotXY).

Load the model. Set the solver type to SSA to perform stochastic simulations, and set the stop time to 3.

sbioloadproject lotka;
cs              = getconfigset(m1);
cs.SolverType   = 'SSA';
cs.StopTime     = 3;
rng('default') % For reproducibility

Set the number of runs and use sbioensemblerun for simulation.

numRuns = 4;
sd      = sbioensemblerun(m1,numRuns);

Plot each simulation run in a separate subplot. By default, sbiosubplot shows the time plot of each species for each run per subplot.

sbiosubplot(sd); 

Plot selected states against each other; in this case, plot the prey population versus the predator population in separate subplots for each run. Use the function plotXY (shown at the end of this example) to plot the simulated y1 (prey) data versus the y2 (predator). Specify the function as a function handle in the sbiosubplot call to plot each run in its own subplot. In this case, the fifth input argument (showLegend) is set to true, which means the fourth input argument (yArgs) is shown as the legend.

If you use the live script file for this example, the plotXY function is already included at the end of the file. Otherwise, you must define the plotXY function at the end of your .m or .mlx file or add it as a file on the MATLAB path.

sbiosubplot(sd,@plotXY,{'y1'},{'y2'},true,'xlabel','y1','ylabel','y2')

Define plotXY Function

sbiosubplot accepts a function handle of a function with the signature:

function functionName(sd,xArgs,yArgs).

The plotXY function plots two selected states against each other. The first input sd is the simulation data (SimBiology SimData object or vector of objects). In this example, xArgs is a cell array containing the name of the species to be plotted on the x-axis, and yArgs is a cell array containing the name of the species to be plotted on the y-axis. However, you can use the inputs xArgs and yArgs in any way in your custom plotting function. No output from the function is necessary.

function plotXY(sd,xArgs,yArgs)
% Select simulation data for each state from each run.
xData = selectbyname(sd,xArgs);
yData = selectbyname(sd,yArgs);
% Plot the species against each other.
plot(xData.Data,yData.Data);
end

Input Arguments

sd — Simulation results

SimData object

Simulation results, specified as a SimData object or vector of SimData objects.

This argument corresponds to the first input of the function referenced by fcnHandle.

Example: simdata

fcnHandle — Function to generate line plots

function handle

Function to generate line plots, specified as a function handle. For an example of a custom function to plot selected species from simulation data, see Plot Selected States from Simulation Data in Subplots.

The function must have the signature:

function functionName(sd,xArgs,yArgs).

The inputs sd, xArgs, and yArgs are the same inputs that you pass in when you call sbiosubplot. No output from the function is necessary.

Example: @plotXY

Data Types: function_handle

xArgs — State names

string vector | cell array of character vectors

State names to plot, specified as a string vector or cell array of character vectors. For instance, you can use xArgs to represent the states to be plotted on the x-axis of your custom plot.

This argument corresponds to the second input of the function referenced by fcnHandle.

Example: {'y1'}

Data Types: cell

yArgs — State names

string vector | cell array of character vectors

State names to plot, specified as a string vector or cell array of character vectors. For instance, you can use yArgs to represent the states to be plotted on the y-axis of your custom plot.

This argument corresponds to the third input of the function referenced by fcnHandle.

Example: {'y2','z'}

Data Types: cell

showLegend — Logical flag to show plot legend

false (default) | true

Logical flag to show the plot legend, specified as true or false. If true, the function shows yArgs as the legend.

Example: true

Data Types: logical

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: 'xlabel','Species A' specifies the x-label of the plot.

xlabel — Label for x-axis

character vector | string

Label for the x-axis of the plot, specified as the comma-separated pair consisting of 'xlabel' and a character vector or string.

Example: 'xlabel','y1'

Data Types: char | string

ylabel — Label for y-axis

character vector | string

Label for the y-axis of the plot, specified as the comma-separated pair consisting of 'ylabel' and a character vector or string.

Example: 'ylabel','y2'

Data Types: char | string

Version History

Introduced in R2008a