Question regarding static graph

[himoto]

Hi @formersbach,
In the example of NFkB model, Can I change the shape or color for each species based on its status, e.g., mRNA and proteins to be enclosed with circles and squares, respectively?

[formersbach]

Yes it's possible, although somewhat tedious.
You will have to define the shape of each node individually. You can get a list of nodes using:

model = create_model('path.to.model')
model.to_graph()
G = model.graph
G.nodes

Then each node can be edited using:

n = G.get_node('nodename')
n.attr["shape"] = "triangle"

#Equivalent to using "-Nshape=paralellogram" in static_plot() :
for node in G.nodes:
    n = G.get_node[node]
    n.attr["shape"] = "paralellogram"

Detailed available attributes can be found in graphviz doc and pygraphviz doc.
Hope this answers your question!

[himoto]

Thank you for your reply!
In the example of NF-kB model,

model.to_graph()
G = model.graph
for sname in model.species:
    n = G.get_node(sname)
    if sname.startswith("m") or sname.startswith("Rna"):
        n.attr["shape"] = "triangle"
    else:
        n.attr["shape"] = "paralellogram"

After running the code above, I got the expected one!
Note that when I run the code:

for node in G.nodes:
    ...

I got TypeError: 'method' object is not iterable

Thank you