Merge pull request #228 from isaacsas/graph-viz

Generation of graphviz graphs

Project.toml

@@ -3,12 +3,14 @@ uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
 version = "5.0.1"
 
 [deps]
+Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 
 [compat]
+Catlab = "0.7.2"
 Latexify = "0.13.5"
 MacroTools = "0.5"
 ModelingToolkit = "3.14"

src/Catalyst.jl

@@ -25,4 +25,11 @@ export dependants, dependents
 # for Latex printing of ReactionSystems
 include("latexify_recipes.jl")
 
+# for making and saving graphs
+import Base.Iterators: flatten
+using Catlab.Graphics.Graphviz
+import Catlab.Graphics.Graphviz: Graph, Edge
+include("graphs.jl")
+export savegraph
+
 end # module

src/graphs.jl

@@ -0,0 +1,45 @@
+# adapted from Petri.jl
+# https://github.com/mehalter/Petri.jl
+
+graph_attrs = Attributes(:rankdir=>"LR")
+node_attrs  = Attributes(:shape=>"plain", :style=>"filled", :color=>"white")
+edge_attrs  = Attributes(:splines=>"splines")
+
+function edgify(δ, i, reverse::Bool)
+    attr = Attributes()
+    return map(δ) do p
+        val = String(p[1].op.name)
+      weight = "$(p[2])"
+      attr = Attributes(:label=>weight, :labelfontsize=>"6")
+      return Edge(reverse ? ["rx_$i", "$val"] :
+                            ["$val", "rx_$i"], attr)
+    end
+end
+
+"""
+    Graph(model::Model)
+
+convert a Model into a GraphViz Graph. Transition are green boxes and states are blue circles. Arrows go from the input states to the output states for each transition.
+"""
+function Graph(model::ReactionSystem)
+    rxs = reactions(model)
+    statenodes = [Node(string(s.name), Attributes(:shape=>"circle", :color=>"#6C9AC3")) for s in species(model)]
+    transnodes = [Node(string("rx_$i"), Attributes(:shape=>"point", :color=>"#E28F41", :width=>".1")) for (i,r) in enumerate(rxs)]
+
+    stmts = vcat(statenodes, transnodes)
+    edges = map(enumerate(rxs)) do (i,r)
+      vcat(edgify(zip(r.substrates,r.substoich), i, false),
+           edgify(zip(r.products,r.prodstoich), i, true))
+    end |> flatten |> collect
+    stmts = vcat(stmts, edges)
+    g = Graphviz.Graph("G", true, stmts, graph_attrs, node_attrs,edge_attrs)
+    return g
+end
+
+
+function savegraph(g::Graph, fname, fmt="png")
+    open(fname, "w") do io
+        run_graphviz(io, g, format=fmt)
+    end 
+    nothing
+end