From 69f69aeb22a732eee8650f03fbe2f401229dc85f Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Thu, 14 Nov 2024 14:23:18 -0500
Subject: [PATCH 01/20] graph init

---
 ext/CatalystGraphMakieExtension.jl            |   8 +-
 .../rn_graph_plot.jl                          | 185 ++++++++++++++++++
 src/network_analysis.jl                       |  35 ++++
 3 files changed, 225 insertions(+), 3 deletions(-)
 create mode 100644 ext/CatalystGraphMakieExtension/rn_graph_plot.jl

diff --git a/ext/CatalystGraphMakieExtension.jl b/ext/CatalystGraphMakieExtension.jl
index ae409b645e..378eb96f3a 100644
--- a/ext/CatalystGraphMakieExtension.jl
+++ b/ext/CatalystGraphMakieExtension.jl
@@ -1,11 +1,13 @@
 module CatalystGraphMakieExtension
 
 # Fetch packages.
-using Catalyst, GraphMakie
+using Catalyst, GraphMakie, Graphs 
 import Catalyst: lattice_plot, lattice_animation, extract_vals
-import Graphs: AbstractGraph, SimpleGraph
+import Graphs: AbstractGraph, SimpleGraph, SimpleDiGraph, SimpleEdge, src, dst, ne, nv 
+import Catalyst: speciesreactiongraph, incidencematgraph
 
 # Creates and exports hc_steady_states function.
 include("CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl")
-
+include("CatalystGraphMakieExtension/rn_graph_plot.jl")
+export SRGraph, ComplexGraph
 end
diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
new file mode 100644
index 0000000000..c9b2864b3c
--- /dev/null
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -0,0 +1,185 @@
+#############
+# Adapted from https://github.com/MakieOrg/GraphMakie.jl/issues/52#issuecomment-1018527479
+#############
+
+"""
+    SRGraphWrap{T}
+
+Wrapper for the species-reaction graph containing edges for rate-dependence on species. Intended to allow plotting of multiple edges. 
+"""
+struct SRGraphWrap{T} <: AbstractGraph{T}
+   g::SimpleDiGraph{T}
+   rateedges::Vector{SimpleEdge}
+end
+
+Base.eltype(g::SRGraphWrap) = eltype(g.g)
+Graphs.edgetype(g::SRGraphWrap) = edgetype(g.g)
+Graphs.has_edge(g::SRGraphWrap, s, d) = has_edge(g.g, s, d)
+Graphs.has_vertex(g::SRGraphWrap, i) = has_vertex(g.g, i)
+Graphs.inneighbors(g::SRGraphWrap{T}, i) where T = inneighbors(g.g, i)
+Graphs.outneighbors(g::SRGraphWrap{T}, i) where T = outneighbors(g.g, i)
+Graphs.ne(g::SRGraphWrap) = length(g.rateedges) + length(Graphs.edges(g.g))
+Graphs.nv(g::SRGraphWrap) = nv(g.g)
+Graphs.vertices(g::SRGraphWrap) = vertices(g.g)
+Graphs.is_directed(g::SRGraphWrap) = is_directed(g.g)
+
+function Graphs.edges(g::SRGraphWrap)
+    return vcat(collect(Graphs.edges(g.g)), g.rateedges)
+end
+
+"""
+    PetriNet(rn::ReactionSystem)
+
+    See the documentation for [`SRGraph`](@ref).
+"""
+function PetriNet(rn::ReactionSystem) 
+    SRGraph(rn)
+end
+
+"""
+    SRGraph(rn::ReactionSystem)
+
+Converts a [`ReactionSystem`](@ref) into a GraphMakie plot of the species reaction graph.
+Reactions correspond to small green circles, and species to blue circles.
+
+Notes:
+- Black arrows from species to reactions indicate reactants, and are labelled
+  with their input stoichiometry.
+- Black arrows from reactions to species indicate products, and are labelled
+  with their output stoichiometry.
+- Red arrows from species to reactions indicate that species is used within the
+  rate expression. For example, in the reaction `k*A, B --> C`, there would be a
+  red arrow from `A` to the reaction node. In `k*A, A+B --> C`, there would be
+  red and black arrows from `A` to the reaction node.
+"""  
+function SRGraph(rn::ReactionSystem; interactive = true) 
+    srg = SRGraphWrap(rn)
+    ns = length(species(rn))
+    nodecolors = vcat([:skyblue3 for i in 1:ns], 
+                      [:green for i in ns+1:nv(srg)])
+    ilabels = vcat(map(s -> String(tosymbol(s, escape=false)), species(rn)),
+                   fill("", nv(srg.g) - ns))
+    nodesizes = vcat([30 for i in 1:ns],
+                     [10 for i in ns+1:nv(srg)])
+
+    ssm = substoichmat(rn); psm = prodstoichmat(rn)
+    # Get stoichiometry of reaction
+    edgelabels = map(Graphs.edges(srg.g)) do e
+        string(src(e) > ns ? 
+            psm[dst(e), src(e)-ns] :
+            ssm[src(e), dst(e)-ns]) 
+    end 
+    edgelabels = vcat(edgelabels, fill("", ne(srg) - ne(srg.g)))
+    edgecolors = vcat([:black for i in 1:ne(srg.g)],
+                      [:red for i in ne(srg.g)+1:ne(srg)])
+
+    f, ax, p = graphplot(srg; 
+             edge_color = edgecolors,
+             elabels = edgelabels, 
+             elabels_rotation = 0,
+             ilabels = ilabels, 
+             node_color = nodecolors,
+             node_size = nodesizes,
+             arrow_shift = :end,
+             arrow_size = 20,
+             curve_distance = 0.1
+            )
+
+    interactive && begin
+        deregister_interaction!(ax, :rectanglezoom)
+        register_interaction!(ax, :ndrag, NodeDrag(p))
+        register_interaction!(ax, :edrag, EdgeDrag(p))
+    end
+    display(f)
+end
+
+# Create the SimpleDiGraph corresponding to the species and reactions
+function SRGraphWrap(rn::ReactionSystem) 
+    srg = speciesreactiongraph(rn)
+    rateedges = Vector{SimpleEdge}()
+    sm = speciesmap(rn); specs = species(rn)
+
+    for (i, rx) in enumerate(reactions(rn)) 
+        deps = get_variables(rx.rate, specs)
+        if deps != Any[]
+            for spec in deps 
+                specidx = sm[spec]
+                push!(rateedges, SimpleEdge(specidx, i + length(specs)))
+            end
+        end
+    end
+    SRGraphWrap(srg, rateedges)
+end
+
+"""
+    ComplexGraph(rn::ReactionSystem)
+
+    Creates a GraphMakie plot of the [`ReactionComplex`](@ref)s in `rn`. Reactions
+    correspond to arrows and reaction complexes to blue circles.
+
+    Notes:
+    - Black arrows from complexes to complexes indicate reactions whose rate is a
+      parameter or a `Number`. i.e. `k, A --> B`.
+    - Red dashed arrows from complexes to complexes indicate reactions whose rate
+    depends on species. i.e. `k*C, A --> B` for `C` a species.
+"""
+function ComplexGraph(rn::ReactionSystem; interactive = true) 
+    img = incidencematgraph(rn)
+    specs = species(rn); rxs = reactions(rn)
+    edgecolors = [:black for i in 1:ne(img)]
+    nodelabels = complexlabels(rn)
+    edgelabels = [repr(rx.rate) for rx in rxs]
+
+    for (i, rx) in enumerate(rxs)
+        deps = get_variables(rx.rate, specs)
+        if deps != Any[]
+            edgecolors[i] = :red
+        end
+    end
+
+    f, ax, p = graphplot(img; 
+             edge_color = edgecolors,
+             elabels = edgelabels, 
+             ilabels = complexlabels(rn), 
+             node_color = :skyblue3,
+             elabels_rotation = 0,
+             arrow_shift = :end, 
+             curve_distance = 0.2
+            )
+
+    interactive && begin
+        deregister_interaction!(ax, :rectanglezoom)
+        register_interaction!(ax, :ndrag, NodeDrag(p))
+        register_interaction!(ax, :edrag, EdgeDrag(p))
+    end
+    display(f)
+end
+
+function complexelemtostr(e::Catalyst.ReactionComplexElement, specstrs) 
+    if e.speciesstoich == 1
+        return "$(specstrs[e.speciesid])"  
+    else
+        return "$(e.speciesstoich)$(specstrs[e.speciesid])"
+    end
+end
+
+# Get the strings corresponding to the reaction complexes
+function complexlabels(rn::ReactionSystem)
+    labels = String[]
+
+    specstrs = map(s -> String(tosymbol(s, escape=false)), species(rn))
+    complexes, B = reactioncomplexes(rn)
+
+    for complex in complexes
+        if isempty(complex) 
+            push!(labels, "∅")
+        elseif length(complex) == 1
+            push!(labels, complexelemtostr(complex[1], specstrs))
+        else
+            elems = map(c -> complexelemtostr(c, specstrs), complex)
+            str = reduce((e1, e2) -> *(e1, " + ", e2), elems[2:end]; init = elems[1])
+            push!(labels, str)
+        end
+    end
+    labels
+end
diff --git a/src/network_analysis.jl b/src/network_analysis.jl
index 93bebe1888..074cd5f6d3 100644
--- a/src/network_analysis.jl
+++ b/src/network_analysis.jl
@@ -314,6 +314,41 @@ function incidencematgraph(incidencemat::SparseMatrixCSC{Int, Int})
     return graph
 end
 
+
+"""
+    speciesreactiongraph(rn::ReactionSystem)
+
+Construct a directed simple graph where there are two types of nodes: species and reactions. 
+An edge from a species to reaction indicates that it is a reactant, and an edge from a reaction
+to a species indicates that it is a product. By default, the species vertices are listed
+first, so the first n indices correspond to species nodes. 
+
+For example,
+```julia
+sir = @reaction_network SIR begin
+    β, S + I --> 2I
+    ν, I --> R
+end
+speciesreactiongraph(sir)
+"""
+function speciesreactiongraph(rn::ReactionSystem) 
+    specs = species(rn)
+    rxs = reactions(rn)
+    sm = speciesmap(rn)
+    s = length(specs); r = length(rxs); nv = s + r
+    
+    adjmat = zeros(Int64, nv, nv)
+    for (i, rx) in enumerate(rxs) 
+        for (spec, stoich) in zip(rx.substrates, rx.substoich)
+            adjmat[sm[spec], s+i] = stoich
+        end
+        for (spec, stoich) in zip(rx.products, rx.prodstoich)
+            adjmat[s+i, sm[spec]] = stoich
+        end
+    end
+    srg = SimpleDiGraph(adjmat)
+end
+
 ### Linkage, Deficiency, Reversibility ###
 
 """

From 79a20d4f281522256395c63f806a47d7586cdd62 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Thu, 14 Nov 2024 15:48:28 -0500
Subject: [PATCH 02/20] up

---
 .../rn_graph_plot.jl                          | 44 ++++++++++++++-----
 1 file changed, 34 insertions(+), 10 deletions(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index c9b2864b3c..93de84cb31 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -24,7 +24,18 @@ Graphs.vertices(g::SRGraphWrap) = vertices(g.g)
 Graphs.is_directed(g::SRGraphWrap) = is_directed(g.g)
 
 function Graphs.edges(g::SRGraphWrap)
-    return vcat(collect(Graphs.edges(g.g)), g.rateedges)
+    edgelist = vcat(collect(Graphs.edges(g.g)), g.rateedges)
+    edgeorder = sortperm(edgelist)
+    edgelist = edgelist[edgeorder]
+end
+
+function gen_distances(g::SRGraphWrap; inc = 0.2) 
+    edgelist = edges(g)
+    distances = zeros(length(edgelist))
+    for i in 2:Base.length(edgelist)
+        edgelist[i] == edgelist[i-1] && (distances[i] = inc)
+    end
+    distances
 end
 
 """
@@ -37,7 +48,7 @@ function PetriNet(rn::ReactionSystem)
 end
 
 """
-    SRGraph(rn::ReactionSystem)
+    SRGraph(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.
@@ -51,8 +62,10 @@ Notes:
   rate expression. For example, in the reaction `k*A, B --> C`, there would be a
   red arrow from `A` to the reaction node. In `k*A, A+B --> C`, there would be
   red and black arrows from `A` to the reaction node.
+- The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot. 
+    Only allowed if `GLMakie` is the loaded Makie backend.
 """  
-function SRGraph(rn::ReactionSystem; interactive = true) 
+function SRGraph(rn::ReactionSystem; interactive = false) 
     srg = SRGraphWrap(rn)
     ns = length(species(rn))
     nodecolors = vcat([:skyblue3 for i in 1:ns], 
@@ -69,9 +82,15 @@ function SRGraph(rn::ReactionSystem; interactive = true)
             psm[dst(e), src(e)-ns] :
             ssm[src(e), dst(e)-ns]) 
     end 
-    edgelabels = vcat(edgelabels, fill("", ne(srg) - ne(srg.g)))
-    edgecolors = vcat([:black for i in 1:ne(srg.g)],
-                      [:red for i in ne(srg.g)+1:ne(srg)])
+    edgecolors = [:black for i in 1:ne(srg)]
+
+    elist = Graphs.edges(srg)
+    for i in 2:length(elist)
+        elist[i] == elist[i-1] && begin
+            edgecolors[i] = :red
+            insert!(edgelabels, i, "")
+        end
+    end
 
     f, ax, p = graphplot(srg; 
              edge_color = edgecolors,
@@ -82,7 +101,8 @@ function SRGraph(rn::ReactionSystem; interactive = true)
              node_size = nodesizes,
              arrow_shift = :end,
              arrow_size = 20,
-             curve_distance = 0.1
+             curve_distance_usage = true,
+             curve_distance = gen_distances(srg)
             )
 
     interactive && begin
@@ -91,6 +111,7 @@ function SRGraph(rn::ReactionSystem; interactive = true)
         register_interaction!(ax, :edrag, EdgeDrag(p))
     end
     display(f)
+    f
 end
 
 # Create the SimpleDiGraph corresponding to the species and reactions
@@ -112,7 +133,7 @@ function SRGraphWrap(rn::ReactionSystem)
 end
 
 """
-    ComplexGraph(rn::ReactionSystem)
+    ComplexGraph(rn::ReactionSystem; interactive=false)
 
     Creates a GraphMakie plot of the [`ReactionComplex`](@ref)s in `rn`. Reactions
     correspond to arrows and reaction complexes to blue circles.
@@ -120,10 +141,12 @@ end
     Notes:
     - Black arrows from complexes to complexes indicate reactions whose rate is a
       parameter or a `Number`. i.e. `k, A --> B`.
-    - Red dashed arrows from complexes to complexes indicate reactions whose rate
+    - Red arrows from complexes to complexes indicate reactions whose rate
     depends on species. i.e. `k*C, A --> B` for `C` a species.
+    - The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot.
+    Only allowed if `GLMakie` is the loaded Makie backend.
 """
-function ComplexGraph(rn::ReactionSystem; interactive = true) 
+function ComplexGraph(rn::ReactionSystem; interactive = false) 
     img = incidencematgraph(rn)
     specs = species(rn); rxs = reactions(rn)
     edgecolors = [:black for i in 1:ne(img)]
@@ -153,6 +176,7 @@ function ComplexGraph(rn::ReactionSystem; interactive = true)
         register_interaction!(ax, :edrag, EdgeDrag(p))
     end
     display(f)
+    f
 end
 
 function complexelemtostr(e::Catalyst.ReactionComplexElement, specstrs) 

From 95cdf8f89695fd5597ad50776605da09ad973d27 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Thu, 14 Nov 2024 14:23:18 -0500
Subject: [PATCH 03/20] graph init

---
 ext/CatalystGraphMakieExtension.jl            |   8 +-
 .../rn_graph_plot.jl                          | 185 ++++++++++++++++++
 src/network_analysis.jl                       |  35 ++++
 3 files changed, 225 insertions(+), 3 deletions(-)
 create mode 100644 ext/CatalystGraphMakieExtension/rn_graph_plot.jl

diff --git a/ext/CatalystGraphMakieExtension.jl b/ext/CatalystGraphMakieExtension.jl
index ae409b645e..378eb96f3a 100644
--- a/ext/CatalystGraphMakieExtension.jl
+++ b/ext/CatalystGraphMakieExtension.jl
@@ -1,11 +1,13 @@
 module CatalystGraphMakieExtension
 
 # Fetch packages.
-using Catalyst, GraphMakie
+using Catalyst, GraphMakie, Graphs 
 import Catalyst: lattice_plot, lattice_animation, extract_vals
-import Graphs: AbstractGraph, SimpleGraph
+import Graphs: AbstractGraph, SimpleGraph, SimpleDiGraph, SimpleEdge, src, dst, ne, nv 
+import Catalyst: speciesreactiongraph, incidencematgraph
 
 # Creates and exports hc_steady_states function.
 include("CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl")
-
+include("CatalystGraphMakieExtension/rn_graph_plot.jl")
+export SRGraph, ComplexGraph
 end
diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
new file mode 100644
index 0000000000..c9b2864b3c
--- /dev/null
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -0,0 +1,185 @@
+#############
+# Adapted from https://github.com/MakieOrg/GraphMakie.jl/issues/52#issuecomment-1018527479
+#############
+
+"""
+    SRGraphWrap{T}
+
+Wrapper for the species-reaction graph containing edges for rate-dependence on species. Intended to allow plotting of multiple edges. 
+"""
+struct SRGraphWrap{T} <: AbstractGraph{T}
+   g::SimpleDiGraph{T}
+   rateedges::Vector{SimpleEdge}
+end
+
+Base.eltype(g::SRGraphWrap) = eltype(g.g)
+Graphs.edgetype(g::SRGraphWrap) = edgetype(g.g)
+Graphs.has_edge(g::SRGraphWrap, s, d) = has_edge(g.g, s, d)
+Graphs.has_vertex(g::SRGraphWrap, i) = has_vertex(g.g, i)
+Graphs.inneighbors(g::SRGraphWrap{T}, i) where T = inneighbors(g.g, i)
+Graphs.outneighbors(g::SRGraphWrap{T}, i) where T = outneighbors(g.g, i)
+Graphs.ne(g::SRGraphWrap) = length(g.rateedges) + length(Graphs.edges(g.g))
+Graphs.nv(g::SRGraphWrap) = nv(g.g)
+Graphs.vertices(g::SRGraphWrap) = vertices(g.g)
+Graphs.is_directed(g::SRGraphWrap) = is_directed(g.g)
+
+function Graphs.edges(g::SRGraphWrap)
+    return vcat(collect(Graphs.edges(g.g)), g.rateedges)
+end
+
+"""
+    PetriNet(rn::ReactionSystem)
+
+    See the documentation for [`SRGraph`](@ref).
+"""
+function PetriNet(rn::ReactionSystem) 
+    SRGraph(rn)
+end
+
+"""
+    SRGraph(rn::ReactionSystem)
+
+Converts a [`ReactionSystem`](@ref) into a GraphMakie plot of the species reaction graph.
+Reactions correspond to small green circles, and species to blue circles.
+
+Notes:
+- Black arrows from species to reactions indicate reactants, and are labelled
+  with their input stoichiometry.
+- Black arrows from reactions to species indicate products, and are labelled
+  with their output stoichiometry.
+- Red arrows from species to reactions indicate that species is used within the
+  rate expression. For example, in the reaction `k*A, B --> C`, there would be a
+  red arrow from `A` to the reaction node. In `k*A, A+B --> C`, there would be
+  red and black arrows from `A` to the reaction node.
+"""  
+function SRGraph(rn::ReactionSystem; interactive = true) 
+    srg = SRGraphWrap(rn)
+    ns = length(species(rn))
+    nodecolors = vcat([:skyblue3 for i in 1:ns], 
+                      [:green for i in ns+1:nv(srg)])
+    ilabels = vcat(map(s -> String(tosymbol(s, escape=false)), species(rn)),
+                   fill("", nv(srg.g) - ns))
+    nodesizes = vcat([30 for i in 1:ns],
+                     [10 for i in ns+1:nv(srg)])
+
+    ssm = substoichmat(rn); psm = prodstoichmat(rn)
+    # Get stoichiometry of reaction
+    edgelabels = map(Graphs.edges(srg.g)) do e
+        string(src(e) > ns ? 
+            psm[dst(e), src(e)-ns] :
+            ssm[src(e), dst(e)-ns]) 
+    end 
+    edgelabels = vcat(edgelabels, fill("", ne(srg) - ne(srg.g)))
+    edgecolors = vcat([:black for i in 1:ne(srg.g)],
+                      [:red for i in ne(srg.g)+1:ne(srg)])
+
+    f, ax, p = graphplot(srg; 
+             edge_color = edgecolors,
+             elabels = edgelabels, 
+             elabels_rotation = 0,
+             ilabels = ilabels, 
+             node_color = nodecolors,
+             node_size = nodesizes,
+             arrow_shift = :end,
+             arrow_size = 20,
+             curve_distance = 0.1
+            )
+
+    interactive && begin
+        deregister_interaction!(ax, :rectanglezoom)
+        register_interaction!(ax, :ndrag, NodeDrag(p))
+        register_interaction!(ax, :edrag, EdgeDrag(p))
+    end
+    display(f)
+end
+
+# Create the SimpleDiGraph corresponding to the species and reactions
+function SRGraphWrap(rn::ReactionSystem) 
+    srg = speciesreactiongraph(rn)
+    rateedges = Vector{SimpleEdge}()
+    sm = speciesmap(rn); specs = species(rn)
+
+    for (i, rx) in enumerate(reactions(rn)) 
+        deps = get_variables(rx.rate, specs)
+        if deps != Any[]
+            for spec in deps 
+                specidx = sm[spec]
+                push!(rateedges, SimpleEdge(specidx, i + length(specs)))
+            end
+        end
+    end
+    SRGraphWrap(srg, rateedges)
+end
+
+"""
+    ComplexGraph(rn::ReactionSystem)
+
+    Creates a GraphMakie plot of the [`ReactionComplex`](@ref)s in `rn`. Reactions
+    correspond to arrows and reaction complexes to blue circles.
+
+    Notes:
+    - Black arrows from complexes to complexes indicate reactions whose rate is a
+      parameter or a `Number`. i.e. `k, A --> B`.
+    - Red dashed arrows from complexes to complexes indicate reactions whose rate
+    depends on species. i.e. `k*C, A --> B` for `C` a species.
+"""
+function ComplexGraph(rn::ReactionSystem; interactive = true) 
+    img = incidencematgraph(rn)
+    specs = species(rn); rxs = reactions(rn)
+    edgecolors = [:black for i in 1:ne(img)]
+    nodelabels = complexlabels(rn)
+    edgelabels = [repr(rx.rate) for rx in rxs]
+
+    for (i, rx) in enumerate(rxs)
+        deps = get_variables(rx.rate, specs)
+        if deps != Any[]
+            edgecolors[i] = :red
+        end
+    end
+
+    f, ax, p = graphplot(img; 
+             edge_color = edgecolors,
+             elabels = edgelabels, 
+             ilabels = complexlabels(rn), 
+             node_color = :skyblue3,
+             elabels_rotation = 0,
+             arrow_shift = :end, 
+             curve_distance = 0.2
+            )
+
+    interactive && begin
+        deregister_interaction!(ax, :rectanglezoom)
+        register_interaction!(ax, :ndrag, NodeDrag(p))
+        register_interaction!(ax, :edrag, EdgeDrag(p))
+    end
+    display(f)
+end
+
+function complexelemtostr(e::Catalyst.ReactionComplexElement, specstrs) 
+    if e.speciesstoich == 1
+        return "$(specstrs[e.speciesid])"  
+    else
+        return "$(e.speciesstoich)$(specstrs[e.speciesid])"
+    end
+end
+
+# Get the strings corresponding to the reaction complexes
+function complexlabels(rn::ReactionSystem)
+    labels = String[]
+
+    specstrs = map(s -> String(tosymbol(s, escape=false)), species(rn))
+    complexes, B = reactioncomplexes(rn)
+
+    for complex in complexes
+        if isempty(complex) 
+            push!(labels, "∅")
+        elseif length(complex) == 1
+            push!(labels, complexelemtostr(complex[1], specstrs))
+        else
+            elems = map(c -> complexelemtostr(c, specstrs), complex)
+            str = reduce((e1, e2) -> *(e1, " + ", e2), elems[2:end]; init = elems[1])
+            push!(labels, str)
+        end
+    end
+    labels
+end
diff --git a/src/network_analysis.jl b/src/network_analysis.jl
index 93bebe1888..074cd5f6d3 100644
--- a/src/network_analysis.jl
+++ b/src/network_analysis.jl
@@ -314,6 +314,41 @@ function incidencematgraph(incidencemat::SparseMatrixCSC{Int, Int})
     return graph
 end
 
+
+"""
+    speciesreactiongraph(rn::ReactionSystem)
+
+Construct a directed simple graph where there are two types of nodes: species and reactions. 
+An edge from a species to reaction indicates that it is a reactant, and an edge from a reaction
+to a species indicates that it is a product. By default, the species vertices are listed
+first, so the first n indices correspond to species nodes. 
+
+For example,
+```julia
+sir = @reaction_network SIR begin
+    β, S + I --> 2I
+    ν, I --> R
+end
+speciesreactiongraph(sir)
+"""
+function speciesreactiongraph(rn::ReactionSystem) 
+    specs = species(rn)
+    rxs = reactions(rn)
+    sm = speciesmap(rn)
+    s = length(specs); r = length(rxs); nv = s + r
+    
+    adjmat = zeros(Int64, nv, nv)
+    for (i, rx) in enumerate(rxs) 
+        for (spec, stoich) in zip(rx.substrates, rx.substoich)
+            adjmat[sm[spec], s+i] = stoich
+        end
+        for (spec, stoich) in zip(rx.products, rx.prodstoich)
+            adjmat[s+i, sm[spec]] = stoich
+        end
+    end
+    srg = SimpleDiGraph(adjmat)
+end
+
 ### Linkage, Deficiency, Reversibility ###
 
 """

From b9e6a27847b56671861e1afb72abd9ae970852f6 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Thu, 14 Nov 2024 15:48:28 -0500
Subject: [PATCH 04/20] up

---
 .../rn_graph_plot.jl                          | 44 ++++++++++++++-----
 1 file changed, 34 insertions(+), 10 deletions(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index c9b2864b3c..93de84cb31 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -24,7 +24,18 @@ Graphs.vertices(g::SRGraphWrap) = vertices(g.g)
 Graphs.is_directed(g::SRGraphWrap) = is_directed(g.g)
 
 function Graphs.edges(g::SRGraphWrap)
-    return vcat(collect(Graphs.edges(g.g)), g.rateedges)
+    edgelist = vcat(collect(Graphs.edges(g.g)), g.rateedges)
+    edgeorder = sortperm(edgelist)
+    edgelist = edgelist[edgeorder]
+end
+
+function gen_distances(g::SRGraphWrap; inc = 0.2) 
+    edgelist = edges(g)
+    distances = zeros(length(edgelist))
+    for i in 2:Base.length(edgelist)
+        edgelist[i] == edgelist[i-1] && (distances[i] = inc)
+    end
+    distances
 end
 
 """
@@ -37,7 +48,7 @@ function PetriNet(rn::ReactionSystem)
 end
 
 """
-    SRGraph(rn::ReactionSystem)
+    SRGraph(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.
@@ -51,8 +62,10 @@ Notes:
   rate expression. For example, in the reaction `k*A, B --> C`, there would be a
   red arrow from `A` to the reaction node. In `k*A, A+B --> C`, there would be
   red and black arrows from `A` to the reaction node.
+- The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot. 
+    Only allowed if `GLMakie` is the loaded Makie backend.
 """  
-function SRGraph(rn::ReactionSystem; interactive = true) 
+function SRGraph(rn::ReactionSystem; interactive = false) 
     srg = SRGraphWrap(rn)
     ns = length(species(rn))
     nodecolors = vcat([:skyblue3 for i in 1:ns], 
@@ -69,9 +82,15 @@ function SRGraph(rn::ReactionSystem; interactive = true)
             psm[dst(e), src(e)-ns] :
             ssm[src(e), dst(e)-ns]) 
     end 
-    edgelabels = vcat(edgelabels, fill("", ne(srg) - ne(srg.g)))
-    edgecolors = vcat([:black for i in 1:ne(srg.g)],
-                      [:red for i in ne(srg.g)+1:ne(srg)])
+    edgecolors = [:black for i in 1:ne(srg)]
+
+    elist = Graphs.edges(srg)
+    for i in 2:length(elist)
+        elist[i] == elist[i-1] && begin
+            edgecolors[i] = :red
+            insert!(edgelabels, i, "")
+        end
+    end
 
     f, ax, p = graphplot(srg; 
              edge_color = edgecolors,
@@ -82,7 +101,8 @@ function SRGraph(rn::ReactionSystem; interactive = true)
              node_size = nodesizes,
              arrow_shift = :end,
              arrow_size = 20,
-             curve_distance = 0.1
+             curve_distance_usage = true,
+             curve_distance = gen_distances(srg)
             )
 
     interactive && begin
@@ -91,6 +111,7 @@ function SRGraph(rn::ReactionSystem; interactive = true)
         register_interaction!(ax, :edrag, EdgeDrag(p))
     end
     display(f)
+    f
 end
 
 # Create the SimpleDiGraph corresponding to the species and reactions
@@ -112,7 +133,7 @@ function SRGraphWrap(rn::ReactionSystem)
 end
 
 """
-    ComplexGraph(rn::ReactionSystem)
+    ComplexGraph(rn::ReactionSystem; interactive=false)
 
     Creates a GraphMakie plot of the [`ReactionComplex`](@ref)s in `rn`. Reactions
     correspond to arrows and reaction complexes to blue circles.
@@ -120,10 +141,12 @@ end
     Notes:
     - Black arrows from complexes to complexes indicate reactions whose rate is a
       parameter or a `Number`. i.e. `k, A --> B`.
-    - Red dashed arrows from complexes to complexes indicate reactions whose rate
+    - Red arrows from complexes to complexes indicate reactions whose rate
     depends on species. i.e. `k*C, A --> B` for `C` a species.
+    - The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot.
+    Only allowed if `GLMakie` is the loaded Makie backend.
 """
-function ComplexGraph(rn::ReactionSystem; interactive = true) 
+function ComplexGraph(rn::ReactionSystem; interactive = false) 
     img = incidencematgraph(rn)
     specs = species(rn); rxs = reactions(rn)
     edgecolors = [:black for i in 1:ne(img)]
@@ -153,6 +176,7 @@ function ComplexGraph(rn::ReactionSystem; interactive = true)
         register_interaction!(ax, :edrag, EdgeDrag(p))
     end
     display(f)
+    f
 end
 
 function complexelemtostr(e::Catalyst.ReactionComplexElement, specstrs) 

From d2223a9a51f74912ab30b92ec165931bf9fdaa99 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:39:26 -0500
Subject: [PATCH 05/20] Update src/network_analysis.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/network_analysis.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/network_analysis.jl b/src/network_analysis.jl
index 074cd5f6d3..ab0c1f99f9 100644
--- a/src/network_analysis.jl
+++ b/src/network_analysis.jl
@@ -331,7 +331,7 @@ sir = @reaction_network SIR begin
 end
 speciesreactiongraph(sir)
 """
-function speciesreactiongraph(rn::ReactionSystem) 
+function species_reaction_graph(rn::ReactionSystem) 
     specs = species(rn)
     rxs = reactions(rn)
     sm = speciesmap(rn)

From 2c36ac39c9c6401e92d84976c6ffb25b651e79b2 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:39:36 -0500
Subject: [PATCH 06/20] Update ext/CatalystGraphMakieExtension/rn_graph_plot.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 93de84cb31..0214b1a527 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -146,7 +146,7 @@ end
     - The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot.
     Only allowed if `GLMakie` is the loaded Makie backend.
 """
-function ComplexGraph(rn::ReactionSystem; interactive = false) 
+function plot_complex_graph(rn::ReactionSystem; interactive = false) 
     img = incidencematgraph(rn)
     specs = species(rn); rxs = reactions(rn)
     edgecolors = [:black for i in 1:ne(img)]

From 952fb39d1d27d56ea03fce1c40d7fafb63b96dfd Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:39:47 -0500
Subject: [PATCH 07/20] Update ext/CatalystGraphMakieExtension/rn_graph_plot.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 0214b1a527..9fbc4c8755 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -201,7 +201,7 @@ function complexlabels(rn::ReactionSystem)
             push!(labels, complexelemtostr(complex[1], specstrs))
         else
             elems = map(c -> complexelemtostr(c, specstrs), complex)
-            str = reduce((e1, e2) -> *(e1, " + ", e2), elems[2:end]; init = elems[1])
+            str = reduce((e1, e2) -> *(e1, " + ", e2), @view elems[2:end]; init = elems[1])
             push!(labels, str)
         end
     end

From 0bf842bb403e7dd93b707880667e57aaea7e9d6d Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:39:59 -0500
Subject: [PATCH 08/20] Update ext/CatalystGraphMakieExtension/rn_graph_plot.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 9fbc4c8755..f6fde86619 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -65,7 +65,7 @@ Notes:
 - The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot. 
     Only allowed if `GLMakie` is the loaded Makie backend.
 """  
-function SRGraph(rn::ReactionSystem; interactive = false) 
+function plot_speciesreaction_graph(rn::ReactionSystem; interactive = false) 
     srg = SRGraphWrap(rn)
     ns = length(species(rn))
     nodecolors = vcat([:skyblue3 for i in 1:ns], 

From 241173ce8d58c646128d393f35d9546aee23c881 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:40:13 -0500
Subject: [PATCH 09/20] Update ext/CatalystGraphMakieExtension/rn_graph_plot.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index f6fde86619..57925688aa 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -86,7 +86,7 @@ function plot_speciesreaction_graph(rn::ReactionSystem; interactive = false)
 
     elist = Graphs.edges(srg)
     for i in 2:length(elist)
-        elist[i] == elist[i-1] && begin
+        if elist[i] == elist[i-1]
             edgecolors[i] = :red
             insert!(edgelabels, i, "")
         end

From 951e16ffd223bc2a8ae8635cf6ec516deab55023 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:40:24 -0500
Subject: [PATCH 10/20] Update ext/CatalystGraphMakieExtension/rn_graph_plot.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 57925688aa..11e70051f1 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -120,9 +120,11 @@ function SRGraphWrap(rn::ReactionSystem)
     rateedges = Vector{SimpleEdge}()
     sm = speciesmap(rn); specs = species(rn)
 
+    deps = Set()
     for (i, rx) in enumerate(reactions(rn)) 
-        deps = get_variables(rx.rate, specs)
-        if deps != Any[]
+        empty!(deps)
+        get_variables!(deps, rx.rate, specs)
+        if !isempty(deps)
             for spec in deps 
                 specidx = sm[spec]
                 push!(rateedges, SimpleEdge(specidx, i + length(specs)))

From 91abcd1aaf22cbb059c2128f779e0d48f124afe2 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:40:52 -0500
Subject: [PATCH 11/20] Update ext/CatalystGraphMakieExtension/rn_graph_plot.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 11e70051f1..0fb833f909 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -181,7 +181,7 @@ function plot_complex_graph(rn::ReactionSystem; interactive = false)
     f
 end
 
-function complexelemtostr(e::Catalyst.ReactionComplexElement, specstrs) 
+function complexelem_tostr(e::Catalyst.ReactionComplexElement, specstrs) 
     if e.speciesstoich == 1
         return "$(specstrs[e.speciesid])"  
     else

From f9d01a3f3e7fb3a437ee9acc0621456dfe49da86 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:41:14 -0500
Subject: [PATCH 12/20] Update ext/CatalystGraphMakieExtension/rn_graph_plot.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 0fb833f909..8acbfc1ef0 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -155,11 +155,11 @@ function plot_complex_graph(rn::ReactionSystem; interactive = false)
     nodelabels = complexlabels(rn)
     edgelabels = [repr(rx.rate) for rx in rxs]
 
+    deps = Set()
     for (i, rx) in enumerate(rxs)
-        deps = get_variables(rx.rate, specs)
-        if deps != Any[]
-            edgecolors[i] = :red
-        end
+        empty!(deps)
+        get_variables!(deps, rx.rate, specs)
+        (!isempty(deps)) && (edgecolors[i] = :red)
     end
 
     f, ax, p = graphplot(img; 

From 5bb1d10be7f989ecbf391a58d624558aed0bce20 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Fri, 15 Nov 2024 12:30:11 -0500
Subject: [PATCH 13/20] up

---
 .../rn_graph_plot.jl                          | 43 +++++++------
 src/network_analysis.jl                       | 24 +++----
 test/extensions/graphmakie.jl                 | 63 +++++++++++++++++++
 3 files changed, 96 insertions(+), 34 deletions(-)
 create mode 100644 test/extensions/graphmakie.jl

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 8acbfc1ef0..f7988c5257 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -12,6 +12,26 @@ struct SRGraphWrap{T} <: AbstractGraph{T}
    rateedges::Vector{SimpleEdge}
 end
 
+# Create the SimpleDiGraph corresponding to the species and reactions
+function SRGraphWrap(rn::ReactionSystem) 
+    srg = speciesreactiongraph(rn)
+    rateedges = Vector{SimpleEdge}()
+    sm = speciesmap(rn); specs = species(rn)
+
+    deps = Set()
+    for (i, rx) in enumerate(reactions(rn)) 
+        empty!(deps)
+        get_variables!(deps, rx.rate, specs)
+        if !isempty(deps)
+            for spec in deps 
+                specidx = sm[spec]
+                push!(rateedges, SimpleEdge(specidx, i + length(specs)))
+            end
+        end
+    end
+    SRGraphWrap(srg, rateedges)
+end
+
 Base.eltype(g::SRGraphWrap) = eltype(g.g)
 Graphs.edgetype(g::SRGraphWrap) = edgetype(g.g)
 Graphs.has_edge(g::SRGraphWrap, s, d) = has_edge(g.g, s, d)
@@ -25,8 +45,7 @@ Graphs.is_directed(g::SRGraphWrap) = is_directed(g.g)
 
 function Graphs.edges(g::SRGraphWrap)
     edgelist = vcat(collect(Graphs.edges(g.g)), g.rateedges)
-    edgeorder = sortperm(edgelist)
-    edgelist = edgelist[edgeorder]
+    edgelist = sort!(edgelist)
 end
 
 function gen_distances(g::SRGraphWrap; inc = 0.2) 
@@ -114,26 +133,6 @@ function plot_speciesreaction_graph(rn::ReactionSystem; interactive = false)
     f
 end
 
-# Create the SimpleDiGraph corresponding to the species and reactions
-function SRGraphWrap(rn::ReactionSystem) 
-    srg = speciesreactiongraph(rn)
-    rateedges = Vector{SimpleEdge}()
-    sm = speciesmap(rn); specs = species(rn)
-
-    deps = Set()
-    for (i, rx) in enumerate(reactions(rn)) 
-        empty!(deps)
-        get_variables!(deps, rx.rate, specs)
-        if !isempty(deps)
-            for spec in deps 
-                specidx = sm[spec]
-                push!(rateedges, SimpleEdge(specidx, i + length(specs)))
-            end
-        end
-    end
-    SRGraphWrap(srg, rateedges)
-end
-
 """
     ComplexGraph(rn::ReactionSystem; interactive=false)
 
diff --git a/src/network_analysis.jl b/src/network_analysis.jl
index ab0c1f99f9..7ffdea0752 100644
--- a/src/network_analysis.jl
+++ b/src/network_analysis.jl
@@ -316,12 +316,12 @@ end
 
 
 """
-    speciesreactiongraph(rn::ReactionSystem)
+    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 to reaction indicates that it is a reactant, and an edge from a reaction
-to a species indicates that it is a product. 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. 
 
 For example,
 ```julia
@@ -329,24 +329,24 @@ sir = @reaction_network SIR begin
     β, S + I --> 2I
     ν, I --> R
 end
-speciesreactiongraph(sir)
+species_reaction_graph(sir)
 """
 function species_reaction_graph(rn::ReactionSystem) 
     specs = species(rn)
     rxs = reactions(rn)
     sm = speciesmap(rn)
-    s = length(specs); r = length(rxs); nv = s + r
+    s = length(specs)
     
-    adjmat = zeros(Int64, nv, nv)
+    edgelist = Graphs.Edge[]
     for (i, rx) in enumerate(rxs) 
-        for (spec, stoich) in zip(rx.substrates, rx.substoich)
-            adjmat[sm[spec], s+i] = stoich
+        for spec in rx.substrates
+            push!(edgelist, Graphs.Edge(sm[spec], s+i))
         end
-        for (spec, stoich) in zip(rx.products, rx.prodstoich)
-            adjmat[s+i, sm[spec]] = stoich
+        for spec in rx.products
+            push!(edgelist, Graphs.Edge(s+i, sm[spec]))
         end
     end
-    srg = SimpleDiGraph(adjmat)
+    srg = Graphs.SimpleDiGraphFromIterator(edgelist)
 end
 
 ### Linkage, Deficiency, Reversibility ###
diff --git a/test/extensions/graphmakie.jl b/test/extensions/graphmakie.jl
new file mode 100644
index 0000000000..659b3051b0
--- /dev/null
+++ b/test/extensions/graphmakie.jl
@@ -0,0 +1,63 @@
+using Catalyst, GraphMakie, GLMakie
+include("../test_networks.jl")
+# Test that speciesreactiongraph is generated correctly
+let
+    brusselator = @reaction_network begin
+        A, ∅ --> X
+        1, 2X + Y --> 3X
+        B, X --> Y
+        1, X --> ∅
+    end
+
+    srg = Catalyst.species_reaction_graph(brusselator)
+    s = length(species(brusselator))
+    edgel = Edge.([(s+1, 1),
+                   (1, s+2),
+                   (2, s+2),
+                   (s+2, 1),
+                   (s+3, 2),
+                   (1, s+3),
+                   (1, s+4)])
+    @test all(∈(collect(Graphs.edges(srg))), edgel)
+
+    MAPK = @reaction_network MAPK begin
+        (k₁, k₂),KKK + E1 <--> KKKE1
+        k₃, KKKE1 --> KKK_ + E1
+        (k₄, k₅), KKK_ + E2 <--> KKKE2
+        k₆, KKKE2 --> KKK + E2
+        (k₇, k₈), KK + KKK_ <--> KK_KKK_
+        k₉, KK_KKK_ --> KKP + KKK_
+        (k₁₀, k₁₁), KKP + KKK_ <--> KKPKKK_
+        k₁₂, KKPKKK_ --> KKPP + KKK_
+        (k₁₃, k₁₄), KKP + KKPase <--> KKPKKPase
+        k₁₅, KKPPKKPase --> KKP + KKPase
+        k₁₆,KKPKKPase --> KK + KKPase
+        (k₁₇, k₁₈), KKPP + KKPase <--> KKPPKKPase
+        (k₁₉, k₂₀), KKPP + K <--> KKPPK
+        k₂₁, KKPPK --> KKPP + KP
+        (k₂₂, k₂₃), KKPP + KP <--> KPKKPP
+        k₂₄, KPKKPP --> KPP + KKPP
+        (k₂₅, k₂₆), KP + KPase <--> KPKPase
+        k₂₇, KKPPKPase --> KP + KPase
+        k₂₈, KPKPase --> K + KPase
+        (k₂₉, k₃₀), KPP + KPase <--> KKPPKPase
+    end
+    srg = Catalyst.species_reaction_graph(MAPK)
+    @test nv(srg) == length(species(MAPK)) + length(reactions(MAPK))
+    @test ne(srg) == 90
+end
+
+# Test that rate edges are inferred correctly
+let
+    rn = @reaction_network begin
+        k, A --> B
+        k * C, A --> C
+        k * B, B --> C
+    end
+    srg = SRGraphWrap(rn)
+    s = length(species(rn))
+    @test Edge(3, s+2) ∈ srg.rateedges 
+    @test Edge(2, s+3) ∈ srg.rateedges 
+    # Since B is both a dep and a reactant
+    @test count(==(Edge(2, s+3)), edges(srg)) == 2
+end

From b2bedf66d48c0f6aa4c07f61228dd14650f8ec3a Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Fri, 15 Nov 2024 14:51:33 -0500
Subject: [PATCH 14/20] fixes

---
 ext/CatalystGraphMakieExtension.jl            |  8 +--
 .../rn_graph_plot.jl                          | 71 +++++++------------
 src/Catalyst.jl                               |  6 ++
 test/extensions/graphmakie.jl                 | 57 +++++++++++++--
 4 files changed, 86 insertions(+), 56 deletions(-)

diff --git a/ext/CatalystGraphMakieExtension.jl b/ext/CatalystGraphMakieExtension.jl
index 378eb96f3a..20c2c1a96f 100644
--- a/ext/CatalystGraphMakieExtension.jl
+++ b/ext/CatalystGraphMakieExtension.jl
@@ -2,12 +2,10 @@ module CatalystGraphMakieExtension
 
 # Fetch packages.
 using Catalyst, GraphMakie, Graphs 
-import Catalyst: lattice_plot, lattice_animation, extract_vals
-import Graphs: AbstractGraph, SimpleGraph, SimpleDiGraph, SimpleEdge, src, dst, ne, nv 
-import Catalyst: speciesreactiongraph, incidencematgraph
+import Catalyst: lattice_plot, lattice_animation, extract_vals, get_variables!
+import Catalyst: species_reaction_graph, incidencematgraph
 
-# Creates and exports hc_steady_states function.
+# Creates and exports graph plotting functions.
 include("CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl")
 include("CatalystGraphMakieExtension/rn_graph_plot.jl")
-export SRGraph, ComplexGraph
 end
diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index f7988c5257..95a99823ef 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -7,15 +7,16 @@
 
 Wrapper for the species-reaction graph containing edges for rate-dependence on species. Intended to allow plotting of multiple edges. 
 """
-struct SRGraphWrap{T} <: AbstractGraph{T}
+struct SRGraphWrap{T} <: Graphs.AbstractGraph{T}
    g::SimpleDiGraph{T}
-   rateedges::Vector{SimpleEdge}
+   rateedges::Vector{Graphs.SimpleEdge{T}}
+   edgeorder::Vector{Int64}
 end
 
 # Create the SimpleDiGraph corresponding to the species and reactions
 function SRGraphWrap(rn::ReactionSystem) 
-    srg = speciesreactiongraph(rn)
-    rateedges = Vector{SimpleEdge}()
+    srg = species_reaction_graph(rn)
+    rateedges = Vector{Graphs.SimpleEdge{Int}}()
     sm = speciesmap(rn); specs = species(rn)
 
     deps = Set()
@@ -25,11 +26,13 @@ function SRGraphWrap(rn::ReactionSystem)
         if !isempty(deps)
             for spec in deps 
                 specidx = sm[spec]
-                push!(rateedges, SimpleEdge(specidx, i + length(specs)))
+                push!(rateedges, Graphs.SimpleEdge(specidx, i + length(specs)))
             end
         end
     end
-    SRGraphWrap(srg, rateedges)
+    edgelist = vcat(collect(Graphs.edges(srg)), rateedges)
+    edgeorder = sortperm(edgelist)
+    SRGraphWrap(srg, rateedges, edgeorder)
 end
 
 Base.eltype(g::SRGraphWrap) = eltype(g.g)
@@ -44,8 +47,7 @@ Graphs.vertices(g::SRGraphWrap) = vertices(g.g)
 Graphs.is_directed(g::SRGraphWrap) = is_directed(g.g)
 
 function Graphs.edges(g::SRGraphWrap)
-    edgelist = vcat(collect(Graphs.edges(g.g)), g.rateedges)
-    edgelist = sort!(edgelist)
+    edgelist = vcat(collect(Graphs.edges(g.g)), g.rateedges)[g.edgeorder]
 end
 
 function gen_distances(g::SRGraphWrap; inc = 0.2) 
@@ -60,14 +62,14 @@ end
 """
     PetriNet(rn::ReactionSystem)
 
-    See the documentation for [`SRGraph`](@ref).
+    See the documentation for [`plot_network`](@ref).
 """
-function PetriNet(rn::ReactionSystem) 
-    SRGraph(rn)
+function Catalyst.plot_petrinet(rn::ReactionSystem) 
+    plot_network(rn)
 end
 
 """
-    SRGraph(rn::ReactionSystem; interactive=false)
+    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.
@@ -81,10 +83,9 @@ Notes:
   rate expression. For example, in the reaction `k*A, B --> C`, there would be a
   red arrow from `A` to the reaction node. In `k*A, A+B --> C`, there would be
   red and black arrows from `A` to the reaction node.
-- The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot. 
-    Only allowed if `GLMakie` is the loaded Makie backend.
 """  
-function plot_speciesreaction_graph(rn::ReactionSystem; interactive = false) 
+# TODO: update docs for interacting with plots. The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot. Only allowed if `GLMakie` is the loaded Makie backend.
+function Catalyst.plot_network(rn::ReactionSystem)
     srg = SRGraphWrap(rn)
     ns = length(species(rn))
     nodecolors = vcat([:skyblue3 for i in 1:ns], 
@@ -103,19 +104,19 @@ function plot_speciesreaction_graph(rn::ReactionSystem; interactive = false)
     end 
     edgecolors = [:black for i in 1:ne(srg)]
 
-    elist = Graphs.edges(srg)
-    for i in 2:length(elist)
-        if elist[i] == elist[i-1]
+    num_e = ne(srg.g)
+    for i in 1:length(srg.edgeorder)
+        if srg.edgeorder[i] > num_e
             edgecolors[i] = :red
             insert!(edgelabels, i, "")
         end
     end
 
-    f, ax, p = graphplot(srg; 
+    graphplot(srg; 
              edge_color = edgecolors,
-             elabels = edgelabels, 
+             elabels = edgelabels,
              elabels_rotation = 0,
-             ilabels = ilabels, 
+             ilabels = ilabels,
              node_color = nodecolors,
              node_size = nodesizes,
              arrow_shift = :end,
@@ -123,18 +124,10 @@ function plot_speciesreaction_graph(rn::ReactionSystem; interactive = false)
              curve_distance_usage = true,
              curve_distance = gen_distances(srg)
             )
-
-    interactive && begin
-        deregister_interaction!(ax, :rectanglezoom)
-        register_interaction!(ax, :ndrag, NodeDrag(p))
-        register_interaction!(ax, :edrag, EdgeDrag(p))
-    end
-    display(f)
-    f
 end
 
 """
-    ComplexGraph(rn::ReactionSystem; interactive=false)
+    plot_complexes(rn::ReactionSystem; interactive=false)
 
     Creates a GraphMakie plot of the [`ReactionComplex`](@ref)s in `rn`. Reactions
     correspond to arrows and reaction complexes to blue circles.
@@ -144,10 +137,8 @@ end
       parameter or a `Number`. i.e. `k, A --> B`.
     - Red arrows from complexes to complexes indicate reactions whose rate
     depends on species. i.e. `k*C, A --> B` for `C` a species.
-    - The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot.
-    Only allowed if `GLMakie` is the loaded Makie backend.
 """
-function plot_complex_graph(rn::ReactionSystem; interactive = false) 
+function Catalyst.plot_complexes(rn::ReactionSystem)
     img = incidencematgraph(rn)
     specs = species(rn); rxs = reactions(rn)
     edgecolors = [:black for i in 1:ne(img)]
@@ -161,7 +152,7 @@ function plot_complex_graph(rn::ReactionSystem; interactive = false)
         (!isempty(deps)) && (edgecolors[i] = :red)
     end
 
-    f, ax, p = graphplot(img; 
+    graphplot(img; 
              edge_color = edgecolors,
              elabels = edgelabels, 
              ilabels = complexlabels(rn), 
@@ -170,14 +161,6 @@ function plot_complex_graph(rn::ReactionSystem; interactive = false)
              arrow_shift = :end, 
              curve_distance = 0.2
             )
-
-    interactive && begin
-        deregister_interaction!(ax, :rectanglezoom)
-        register_interaction!(ax, :ndrag, NodeDrag(p))
-        register_interaction!(ax, :edrag, EdgeDrag(p))
-    end
-    display(f)
-    f
 end
 
 function complexelem_tostr(e::Catalyst.ReactionComplexElement, specstrs) 
@@ -199,9 +182,9 @@ function complexlabels(rn::ReactionSystem)
         if isempty(complex) 
             push!(labels, "∅")
         elseif length(complex) == 1
-            push!(labels, complexelemtostr(complex[1], specstrs))
+            push!(labels, complexelem_tostr(complex[1], specstrs))
         else
-            elems = map(c -> complexelemtostr(c, specstrs), complex)
+            elems = map(c -> complexelem_tostr(c, specstrs), complex)
             str = reduce((e1, e2) -> *(e1, " + ", e2), @view elems[2:end]; init = elems[1])
             push!(labels, str)
         end
diff --git a/src/Catalyst.jl b/src/Catalyst.jl
index 047747da71..69da5d8d98 100644
--- a/src/Catalyst.jl
+++ b/src/Catalyst.jl
@@ -167,6 +167,12 @@ export hc_steady_states
 function make_si_ode end
 export make_si_ode
 
+# GraphMakie
+function plot_network end
+function plot_petrinet end
+function plot_complexes end
+export plot_network, plot_complexes, plot_petrinet
+
 ### Spatial Reaction Networks ###
 
 # Spatial reactions.
diff --git a/test/extensions/graphmakie.jl b/test/extensions/graphmakie.jl
index 659b3051b0..e74b6ce48b 100644
--- a/test/extensions/graphmakie.jl
+++ b/test/extensions/graphmakie.jl
@@ -1,5 +1,6 @@
-using Catalyst, GraphMakie, GLMakie
+using Catalyst, GraphMakie, GLMakie, Graphs
 include("../test_networks.jl")
+
 # Test that speciesreactiongraph is generated correctly
 let
     brusselator = @reaction_network begin
@@ -11,7 +12,7 @@ let
 
     srg = Catalyst.species_reaction_graph(brusselator)
     s = length(species(brusselator))
-    edgel = Edge.([(s+1, 1),
+    edgel = Graphs.Edge.([(s+1, 1),
                    (1, s+2),
                    (2, s+2),
                    (s+2, 1),
@@ -45,19 +46,61 @@ let
     srg = Catalyst.species_reaction_graph(MAPK)
     @test nv(srg) == length(species(MAPK)) + length(reactions(MAPK))
     @test ne(srg) == 90
+
+    # Test that figures are generated properly. 
+    f = plot_network(MAPK)
+    save("fig.png", f)
+    @test isfile("fig.png")
+    rm("fig.png")
+    f = plot_network(brusselator)
+    save("fig.png", f)
+    @test isfile("fig.png")
+    rm("fig.png")
+
+    f = plot_complexes(MAPK); save("fig.png", f)
+    @test isfile("fig.png")
+    rm("fig.png")
+    f = plot_complexes(brusselator); save("fig.png", f)
+    @test isfile("fig.png")
+    rm("fig.png")
 end
 
-# Test that rate edges are inferred correctly
+CGME = Base.get_extension(parentmodule(ReactionSystem), :CatalystGraphMakieExtension)
+# Test that rate edges are inferred correctly. We should see two for the following reaction network. 
 let
+    # Two rate edges, one to species and one to product
     rn = @reaction_network begin
         k, A --> B
         k * C, A --> C
         k * B, B --> C
     end
-    srg = SRGraphWrap(rn)
+    srg = CGME.SRGraphWrap(rn)
     s = length(species(rn))
-    @test Edge(3, s+2) ∈ srg.rateedges 
-    @test Edge(2, s+3) ∈ srg.rateedges 
+    @test ne(srg) == 8
+    @test Graphs.Edge(3, s+2) ∈ srg.rateedges 
+    @test Graphs.Edge(2, s+3) ∈ srg.rateedges 
     # Since B is both a dep and a reactant
-    @test count(==(Edge(2, s+3)), edges(srg)) == 2
+    @test count(==(Graphs.Edge(2, s+3)), edges(srg)) == 2
+
+    f = plot_network(rn)
+    save("fig.png", f)
+    @test isfile("fig.png")
+    rm("fig.png")
+    f = plot_complexes(rn); save("fig.png", f)
+    @test isfile("fig.png")
+    rm("fig.png")
+
+    # Two rate edges, both to reactants 
+    rn = @reaction_network begin
+        k, A --> B
+        k * A, A --> C
+        k * B, B --> C
+    end
+    srg = CGME.SRGraphWrap(rn)
+    s = length(species(rn))
+    @test ne(srg) == 8
+    # Since A, B is both a dep and a reactant
+    @test count(==(Graphs.Edge(1, s+2)), edges(srg)) == 2
+    @test count(==(Graphs.Edge(2, s+3)), edges(srg)) == 2
 end
+

From 21237a88ad5c132c0366b2e43394ff1511f7ba44 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Fri, 15 Nov 2024 15:00:09 -0500
Subject: [PATCH 15/20] up

---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 95a99823ef..1792ed039e 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -60,7 +60,7 @@ function gen_distances(g::SRGraphWrap; inc = 0.2)
 end
 
 """
-    PetriNet(rn::ReactionSystem)
+    plot_petrinet(rn::ReactionSystem)
 
     See the documentation for [`plot_network`](@ref).
 """

From 794fb04418c4555e58170a583cb1508c130471da Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:39:08 -0500
Subject: [PATCH 16/20] Update ext/CatalystGraphMakieExtension.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 ext/CatalystGraphMakieExtension.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ext/CatalystGraphMakieExtension.jl b/ext/CatalystGraphMakieExtension.jl
index 20c2c1a96f..d9c20aec14 100644
--- a/ext/CatalystGraphMakieExtension.jl
+++ b/ext/CatalystGraphMakieExtension.jl
@@ -1,8 +1,8 @@
 module CatalystGraphMakieExtension
 
 # Fetch packages.
-using Catalyst, GraphMakie, Graphs 
-import Catalyst: lattice_plot, lattice_animation, extract_vals, get_variables!
+using Catalyst, GraphMakie, Graphs, Symbolics
+using Symbolics: get_variables!
 import Catalyst: species_reaction_graph, incidencematgraph
 
 # Creates and exports graph plotting functions.

From 161d1b6ca5738cfa22e41f54cfd4c16b1e41ed4f Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:40:59 -0500
Subject: [PATCH 17/20] Update src/Catalyst.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/Catalyst.jl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Catalyst.jl b/src/Catalyst.jl
index 69da5d8d98..4afc8a29a3 100644
--- a/src/Catalyst.jl
+++ b/src/Catalyst.jl
@@ -169,7 +169,6 @@ export make_si_ode
 
 # GraphMakie
 function plot_network end
-function plot_petrinet end
 function plot_complexes end
 export plot_network, plot_complexes, plot_petrinet
 

From ef0635fae6558aea6112f640f4263c77f8ddba99 Mon Sep 17 00:00:00 2001
From: Vincent Du <54586336+vyudu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 10:41:09 -0500
Subject: [PATCH 18/20] Update src/Catalyst.jl

Co-authored-by: Sam Isaacson <isaacsas@users.noreply.github.com>
---
 src/Catalyst.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Catalyst.jl b/src/Catalyst.jl
index 4afc8a29a3..ad12f0fa4b 100644
--- a/src/Catalyst.jl
+++ b/src/Catalyst.jl
@@ -170,7 +170,7 @@ export make_si_ode
 # GraphMakie
 function plot_network end
 function plot_complexes end
-export plot_network, plot_complexes, plot_petrinet
+export plot_network, plot_complexes
 
 ### Spatial Reaction Networks ###
 

From a46a0c573f3bb3e99c339e260244398b92f75a4e Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Sat, 16 Nov 2024 10:43:24 -0500
Subject: [PATCH 19/20] up

---
 ext/CatalystGraphMakieExtension/rn_graph_plot.jl | 14 +++-----------
 src/network_analysis.jl                          |  9 ++++++---
 2 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 1792ed039e..644a175b32 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/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
diff --git a/src/network_analysis.jl b/src/network_analysis.jl
index 7ffdea0752..86802fb919 100644
--- a/src/network_analysis.jl
+++ b/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

From 82a575d67938a1df4e8f79cbeb3baa44114fa4dd Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Sat, 16 Nov 2024 11:09:12 -0500
Subject: [PATCH 20/20] fix

---
 ext/CatalystGraphMakieExtension.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/CatalystGraphMakieExtension.jl b/ext/CatalystGraphMakieExtension.jl
index d9c20aec14..a47ef7f5e5 100644
--- a/ext/CatalystGraphMakieExtension.jl
+++ b/ext/CatalystGraphMakieExtension.jl
@@ -3,7 +3,7 @@ module CatalystGraphMakieExtension
 # Fetch packages.
 using Catalyst, GraphMakie, Graphs, Symbolics
 using Symbolics: get_variables!
-import Catalyst: species_reaction_graph, incidencematgraph
+import Catalyst: species_reaction_graph, incidencematgraph, lattice_plot, lattice_animation
 
 # Creates and exports graph plotting functions.
 include("CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl")