Storing networkx graph object with non-unique nodes as graphviz file

Question

I want to store in graphviz file a networkx object that has non-unique nodes. I have created non-unique nodes in networkx using labels. But it's just able to display the nodes with non-unique labels.

G = nx.MultiDiGraph()
G.add_node(0)
G.add_node(1)
G.add_node(2)
labels = {0: 'a', 1: 'b', 2: 'a'}
pos=nx.spring_layout(G)
nx.draw_networkx_nodes(G,pos)
nx.draw_networkx_edges(G,pos)
nx.draw_networkx_labels(MG,pos,labels,font_size=16)

This gives return value of last statement and the output:


return value: {0: Text(-0.6135625730904766, -0.6074010681652476, 'a'),
 1: Text(0.9319946933900001, -0.3925989318347525, 'b'),
 2: Text(-0.31843212029952345, 1.0, 'a')}

networkx output

Is there a way to take this output from draw_networkx_labels and use it to create graphviz file. I need non-unique nodes in graphviz file output. I'm trying to do something like below:

x = nx.draw_networkx_labels(G,pos,labels,font_size=16)
write_dot(x, "dot.gv")
s = Source.from_file('dot.gv')
s.view()

This will throw error as nx.draw_networkx_labels does not return the object it prints above. If I just use G object, it will not use labels 'a' and 'b'. Also, is there a simpler way to create non-unique nodes in networkx?

score 1 · Accepted Answer · answered Nov 04 '19 at 09:11

You are confusing nodes with node labels. It doesn't make sense to add duplicate nodes in a graph. However, you can add non-unique labels to existing nodes of in a Graph.

Take a look at this code:

import networkx as nx

G = nx.MultiDiGraph()
G.add_nodes_from(list(range(5)))

labels = {
    0: 'a',
    1: 'b',
    2: 'a',
    3: 'c',
    4: 'd'}

G.add_edge(0, 1)
G.add_edge(2, 1)
G.add_edge(3, 2)
G.add_edge(3, 4)

# Add the labels as a separate attribute in each node
nx.set_node_attributes(G, labels, 'label')

pos=nx.spring_layout(G)
nx.draw_networkx_nodes(G,pos)
nx.draw_networkx_edges(G,pos)
nx.draw_networkx_labels(G,pos,labels,font_size=16)

Now coming to saving the graph in a graphviz file format:

from networkx.drawing.nx_agraph import write_dot
from graphviz import Source

write_dot(G, "dot.gv")
Source.from_file('dot.gv')

As you can see as per your question, the label names are preserved. You can further read the pygraphviz documentation to further manipulate the graph you have obtained.

References:

You can check out this Google Colab notebook for the code shown above.

Storing networkx graph object with non-unique nodes as graphviz file

1 Answers1