Basics

The plotting defaults provided by BioSimulator.jl require the Plots.jl package. You can install it with

Pkg.add("Plots")

BioSimulator.jl does not load the Plots.jl package by default. Any time you need plotting functionality, simply load the package:

# if BioSimulator is already loaded
using Plots

# if you're just starting
using BioSimulator, Plots

Note that Plots.jl is independent of BioSimulator.jl. Please consult the Plots.jl documentation for additional details.

BioSimulator.jl provides a few plotting recipes to quickly summarize simulation results. The type of plot is controlled by a summary keyword. The available options include:

summary = :trajectory: An individual SamplePath.
summary = :mean: Averaged trajectories based on an Ensemble.
summary = :histogram: A histogram based on an Ensemble.
summary = :phase: A phase portrait of the stochastic system. The default puts the first component on $x$-axis and the second component on the $y-$axis.

See the following examples on how to use the default recipes.

Sample trajectories

# `result` is an `Ensemble` of 100 trajectories
plot(result[1], summary = :trajectory,
    xlabel = "time", ylabel = "count",
    label = ["gene" "P2_gene" "mRNA" "P" "P2"])

Mean trajectories

# select data for protein `P` and dimer `P2` with their indices
plot(result, summary = :mean,
    xlabel = "time", ylabel = "average",
    vars = [4,5], label = ["P" "P2"])

Distributions

# 3 figures on top row, 2 on the bottom
mylayout = @layout [a{0.33w} a{0.33w} a{0.33w}
                        a{0.5w} a{0.5w}]

plot(result, summary = :histogram,
    ylabel = "probability",
    timepoint = 500.0, normalize = :probability, bins = :sturges,
    layout = mylayout,
    label = ["gene" "P2_gene" "mRNA" "P" "P2"])

Phase plots

For a SamplePath:

plot(result[1], summary = :phase,
    vars = (4,5), xlabel = "P", ylabel = "P2", colorbar = true)

For an Ensemble:

plot(result, summary = :phase,
    vars = (4,5), xlabel = "P", ylabel = "P2", colorbar = true)

Configurations (Lattice-based models)

You can visualize individual configurations in 2D or 3D:

plot(result[10])

A SamplePath is visualized by plotting the initial and final configuration:

plot(result)

General tips

The components of a SamplePath follow the same order in the Network definition. For example, if we define X, Y, and Z in our model, then their indices are 1, 2, and 3, respectively.
By default, every variable will appear in a plot (except for phase portraits). You can select a few variables using the var keyword argument.