up

Author: vyudu

ext/CatalystGraphMakieExtension/rn_graph_plot.jl

@@ -59,20 +59,12 @@ function gen_distances(g::SRGraphWrap; inc = 0.2)
     distances
 end
 
-"""
-    plot_petrinet(rn::ReactionSystem)
-
-    See the documentation for [`plot_network`](@ref).
-"""
-function Catalyst.plot_petrinet(rn::ReactionSystem) 
-    plot_network(rn)
-end
-
 """
     plot_network(rn::ReactionSystem; interactive=false)
 
-Converts a [`ReactionSystem`](@ref) into a GraphMakie plot of the species reaction graph.
-Reactions correspond to small green circles, and species to blue circles.
+Converts a [`ReactionSystem`](@ref) into a GraphMakie plot of the species reaction graph
+(or Petri net representation). Reactions correspond to small green circles, and 
+species to blue circles.
 
 Notes:
 - Black arrows from species to reactions indicate reactants, and are labelled

src/network_analysis.jl

@@ -319,9 +319,12 @@ end
     species_reaction_graph(rn::ReactionSystem)
 
 Construct a directed simple graph where there are two types of nodes: species and reactions. 
-An edge from a species *s* to reaction *r* indicates that *s* is a reactant for *r*, and an edge from a reaction
-r to a species s indicates that *s* is a product of *r*. By default, the species vertices are listed
-first, so the first *n* indices correspond to species nodes. 
+An edge from a species *s* to reaction *r* indicates that *s* is a reactant for *r*, and 
+an edge from a reaction *r* to a species *s* indicates that *s* is a product of *r*. By 
+default, the species vertices are listed first, so the first *n* indices correspond to 
+species nodes. 
+
+Note: this is equivalent to the Petri net representation of a chemical reaction network.
 
 For example,
 ```julia