fix graph defaults

Author: vyudu

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

@@ -88,18 +88,16 @@ 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 show 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
-showdecorations!(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()
-display(F)
+display(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. 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)
-ax.aspect = DataAspect()
 ax.title = "Brusselator"
 display(f)
 ```

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

@@ -210,6 +210,7 @@ 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
@@ -266,8 +267,9 @@ function Catalyst.plot_complexes(rn::ReactionSystem; show_rate_labels = false, k
     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