Fix graph defaults, plotting graphs

Project.toml

@@ -32,12 +32,13 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
 
 [extensions]
 CatalystBifurcationKitExtension = "BifurcationKit"
 CatalystCairoMakieExtension = "CairoMakie"
-CatalystGraphMakieExtension = ["GraphMakie", "NetworkLayout"]
+CatalystGraphMakieExtension = ["GraphMakie", "NetworkLayout", "Makie"]
 CatalystHomotopyContinuationExtension = "HomotopyContinuation"
 
 [compat]
@@ -56,6 +57,7 @@ JumpProcesses = "9.13.2"
 LaTeXStrings = "1.3.0"
 Latexify = "0.16.6"
 MacroTools = "0.5.5"
+Makie = "0.22.1"
 ModelingToolkit = "< 9.60"
 NetworkLayout = "0.4.7"
 Parameters = "0.12"

docs/src/model_creation/model_visualisation.md

@@ -88,34 +88,34 @@ In this section we demonstrate some of the ways that plot objects can be manipul
 f, ax, p = plot_complexes(brusselator, show_rate_labels = true)
 ```
 
-It seems like a bit of the top node is cut off. Let's hide the tick marks and grid and increase the top and bottom margins by increasing `yautolimitmargin`.
+It seems like a bit of the top node is cut off. Let's increase the top and bottom margins by increasing `yautolimitmargin`.
 ```@example visualisation_graphs
-hidedecorations!(ax)
-ax.yautolimitmargin = (0.1, 0.1) # defaults to (0.05, 0.05)
+ax.yautolimitmargin = (0.3, 0.3) # defaults to (0.15, 0.15)
 ax.aspect = DataAspect()
+f
 ```
 
-There are many keyword arguments that can be passed to `plot_network` or `plot_complexes` to change the look of the graph (which get passed to the `graphplot` Makie recipe). Let's change the color of the nodes and make the inner labels a bit smaller. As before, we hide the tick marks and grid. Let's also give the plot a title. 
+There are many keyword arguments that can be passed to `plot_network` or `plot_complexes` to change the look of the graph (which get passed to the `graphplot` Makie recipe). Let's change the color of the nodes and make the inner labels a bit smaller. Let's also give the plot a title. 
 ```@example visualisation_graphs
 f, ax, p = plot_complexes(brusselator, show_rate_labels = true, node_color = :yellow, ilabels_fontsize = 10)
-hidedecorations!(ax)
-ax.yautolimitmargin = (0.1, 0.1) # defaults to (0.05, 0.05)
-ax.aspect = DataAspect()
 ax.title = "Brusselator"
+f
 ```
 
 Most of the kwargs that modify the nodes or edges will also accept a vector with the same length as the number of nodes or edges, respectively. See [here](https://graph.makie.org/stable/#The-graphplot-Recipe) for a full list of keyword arguments to `graph_plot`. Note that `plot_complexes` and `plot_network` default to `layout = Stress()` rather than `layout = Spring()`, since `Stress()` is better at generating plots with fewer edge crossings. More layout options and customizations (such as pinning nodes to certain positions) can be found in the [`NetworkLayout` documentation](https://juliagraphs.org/NetworkLayout.jl/stable/).
 
 Once a graph is already created we can also change the keyword arguments by modifying the fields of the `Plot` object `p`.
 ```@example visualisation_graphs
 p.node_color = :orange
+f
 ```
 
 Custom node positions can also be given, if the automatic layout is unsatisfactory.
 ```@example visualisation_graphs
 fixedlayout = [(0,0), (1,0), (0,1), (1,1), (2,0)]
 p.layout = fixedlayout
 autolimits!(ax)
+f
 ```
 
 Makie graph plots can be made to be interactive, allowing one to drag nodes and edges. To do this, we retrieve the axis from the GraphMakie plot, and then register the interactions. **Note that this can only be done if `GLMakie` is the installed Makie backend. See the [GraphMakie docs](https://graph.makie.org/stable/#Predefined-Interactions) for more information about the types of interactions one can register.** Below is a non-interactive code example that shows how to do this:

ext/CatalystGraphMakieExtension.jl

@@ -1,7 +1,7 @@
 module CatalystGraphMakieExtension
 
 # Fetch packages.
-using Catalyst, GraphMakie, Graphs, Symbolics, SparseArrays, NetworkLayout
+using Catalyst, GraphMakie, Graphs, Symbolics, SparseArrays, NetworkLayout, Makie
 using Symbolics: get_variables!
 import Catalyst: species_reaction_graph, incidencematgraph, lattice_plot, lattice_animation
 

ext/CatalystGraphMakieExtension/rn_graph_plot.jl

@@ -209,6 +209,9 @@ function Catalyst.plot_network(rn::ReactionSystem; kwargs...)
 
     f.axis.xautolimitmargin = (0.15, 0.15)
     f.axis.yautolimitmargin = (0.15, 0.15)
+    hidedecorations!(f.axis)
+    hidespines!(f.axis)
+    f.axis.aspect = DataAspect()
 
     f
 end
@@ -260,9 +263,13 @@ function Catalyst.plot_complexes(rn::ReactionSystem; show_rate_labels = false, k
               curve_distance = gen_distances(cg),
               kwargs...
             )
+
     f.axis.xautolimitmargin = (0.15, 0.15)
     f.axis.yautolimitmargin = (0.15, 0.15)
-
+    hidedecorations!(f.axis)
+    hidespines!(f.axis)
+    f.axis.aspect = DataAspect()
+
     f
 end