Simulation plotting doc

docs/pages.jl

@@ -25,7 +25,7 @@ pages = Any[
     ],
     "Model simulation" => Any[
         # Simulation introduction.
-        # Simulation plotting.
+        "model_simulation/simulation_plotting.md",
         "model_simulation/simulation_structure_interfacing.md",
         "model_simulation/TOBEREMOVED_advanced_simulations.md",# Monte Carlo/Ensemble simulations.        
         # Stochastic simulation statistical analysis.

docs/src/model_simulation/simulation_plotting.md

@@ -0,0 +1,87 @@
+# [Simulation_plotting](@id simulation_plotting)
+Catalyst uses the [Plots.jl](https://github.com/JuliaPlots/Plots.jl) package for performing all plots. This section provides a brief summary of some useful plotting options, while [Plots.jl's documentation](https://docs.juliaplots.org/stable/) provides a more throughout description of how to tune your plots.
+
+!!! note
+    [Makie.jl](https://github.com/MakieOrg/Makie.jl) is a popular alternative to the Plots.jl package. While it is not used within Catalyst's documentation, it is worth considering (especially for users interested in interactivity, or increased control over their plots).
+
+## [Common plotting options](@id simulation_plotting_options)
+Let us consider the oscillating [Brusselator](@ref ref) model. We have previously shown how model simulation solutions can be plotted using the `plot` function. Here we plot an ODE simulation from the [Brusselator](@ref ref) model:
+```@example simulation_plotting
+using Catalyst, OrdinaryDiffEq, Plots
+
+brusselator = @reaction_network begin
+    A, ∅ --> X
+    1, 2X + Y --> 3X
+    B, X --> Y
+    1, X --> ∅
+end
+u0 = [:X => 1.0, :Y => 0.0]
+tspan = (0.0, 50.0)
+ps = [:A => 1.0, :B => 4.0]
+
+oprob = ODEProblem(brusselator, u0, tspan, ps)
+sol = solve(oprob)
+plot(sol)
+```
+
+Various plotting options can be provided as optional arguments to the `plot` command. Common options include:
+- `lw`: Determine plot line widths.
+- `la`: Determine plot line's transparency (at `la = 0.0` lines are fully transparent, i.e. not visible).
+- `linestyle`: Determines plot line style.
+- `color`: Determines the line colours.
+- `legend`: Determines the position of the legend/labels.
+- `label`: Determines label texts.
+- `xguide`, `yguide`: Determines x and y axis labels.
+- `title`: Determines plot title.
+- `legendfontsize`, `guidefontsize`, `titlefontsize`: Determines the font size of the labels, x and y guides, and title, respectively.
+
+Here, we re-plot our simulations, utilising some of these options (`legend = :none` is used to disable the legends).
+```@example simulation_plotting
+plot(sol; lw = 4, linestyle = :dash, color = :green, xguide = "Time", yguide = "Concentration", guidefontsize = 14)
+```
+Note that, by default, Catalyst uses `xguide = "t"`. Here, however, we modify this to `xguide = "Time"`. We also note that the `color = :green` change both lines' colours to green. To set different colours for each line, we provide these as *a vector without `,` in-between elements* (in Julia interpreted as a matrix with its first dimension equal to `1`):
+```@example simulation_plotting
+plot(sol; lw = 4, color = [:green :purple])
+```
+A full list of available colours can be found [here](https://juliagraphics.github.io/Colors.jl/stable/namedcolors/). A full list of possible plotting options can be found [here](https://docs.juliaplots.org/stable/attributes/) (look at the list of various plot attributes, e.g. "Series Attributes"). if there is some option(s) you intend to use multiple times, you can call the `default` function using these, in which case they will be used for all subsequent plots. E.g. here:
+```@example simulation_plotting
+default(framestyle = :box, grid = false)
+```
+we designate a box-style frame, and remove the faint background grid, for all subsequent plots in this tutorial.
+
+A useful option unique to Catalyst (and other DifferentialEquations.jl-based) plots is `idxs`. Its input is a vector, listing all the species (or quantities) that should be plotted. I.e.
+```@example simulation_plotting
+plot(sol; idxs = [:X])
+```
+can be used to plot `X` only. When only a single argument is given, the vector form is unnecessary (e.g. `idxs = :X` could have been used instead). If [symbolic species representation is used](@ref ref), this can be used to designate any algebraic expression(s) that should be plotted. E.g. here we plot the total concentration of $X + Y$ throughout the simulation:
+```@example simulation_plotting
+plot(sol; idxs = brusselator.X + brusselator.Y)
+```
+
+## [Multi-plot plots](@id simulation_plotting_options)
+It is possible to save plots in variables. These can then be used as input to the `plot` command. Here, the plot command can be used to create plots containing multiple plots (by providing multiple inputs). E.g. here we plot the concentration of `X` and `Y` in separate subplots:
+```@example simulation_plotting
+plt_X = plot(sol; idxs = [:X])
+plt_Y = plot(sol; idxs = [:Y])
+plot(plt_X, plt_Y)
+```
+
+When working with subplots, the [`layout`](https://docs.juliaplots.org/latest/layouts/) and [`size`](https://docs.juliaplots.org/latest/generated/attributes_plot/) options are typically useful. Here we use `layout` to put the first plot above the second one, and `size` to reshape the plot size:
+```@example simulation_plotting
+plot(plt_X, plt_Y; layout = (2,1), size = (700,500))
+```
+
+## [Saving plots](@id simulation_plotting_options)
+Once a plot has been saved to a variable, the `savefig` function can be used to save it to a file. Here we save our Brusselator plot simulation (the first argument) to a file called "saved_plot.png" (the second argument):
+```@example simulation_plotting
+plt = plot(sol)
+savefig(plt, "saved_plot.png")
+rm("saved_plot.png") # hide
+```
+The plot file type is automatically determined from the extension (if none is given, a .png file is created).
+
+## [Phase-space plots](@id simulation_plotting_options)
+By default, simulations are plotted as species concentrations over time. However, [phase space](https://en.wikipedia.org/wiki/Phase_space#:~:text=In%20dynamical%20systems%20theory%20and,point%20in%20the%20phase%20space.) plots are also possible. This is done by designating the axis arguments using the `idxs` option, but providing them as a tuple. E.g. here we plot our simulation in $X-Y$ space:
+```@example simulation_plotting
+plot(sol; idxs = (:X, :Y))
+```