python - networkx - graph different colored nodes using two lists

Question

I\'m new to networkx and need some help. I\'ve searched previously and couldn\'t resolve my issue. I have a networkx graphviz image I made, using a list as input for the nod

Answer 1

Here is what i used for coloring my graph.

## assign a node attribute, which I am going to color according to
for node in G.nodes():
    G.node[node]['category'] = my_category_dict[node]
## put together a color map, one color for a category
color_map = {'type_A':'b', 'type_B':'#FF0099', 'type_C':'#660066'} 
## construct a list of colors then pass to node_color
nx.draw(G, node_color=[color_map[G.node[node]['category']] for node in G])
plt.show()

And then I got my image as below. I used more colors than in the example. Is this what you want?

Also, this page has lots of examples that I found useful when plotting my graph.

Answer 2

THanks, sophiad for your reply. It seems the answer I was looking for was right in from of my nose the whole time. I needed to make a list of the colors to pass to nx.draw_graphviz.

So, the correct code (that I found) to pass a certain color to a node comparing two lists:

colors=[]
for n in nodes:
    if n in hybrids:
        colors.append('g')
    else:
        colors.append('b')

nx.draw_graphviz(g, prog="fdp", node_color = colors, node_size = sizes)

And for changed the text version, to mirror the color node version, all I had to do was change A.layout() to A.layout(prog="fdp")

And it does not change the layout!

The original image:

The new image:

The new text version:

Answer 3

Ok, SO I've almost got it. I was able to change the color of the nodes I wanted, however it did not keep the same shape of the graph, and I was also able to update the agraph to represent the graphviz fdp format. If anyone is interested here are some changes:

with open(counts, "r") as f2:
        countsdic = defaultdict(list)
        for line in f2:
                k,v = line.strip().split()
                countsdic[k].append(v)

with open(hybrids, "r") as f3:
        hybrids = [line.strip() for line in f3]

print hybrids
tmp = []

for el in sum(edges, []):
        tmp.append(el)

nodes = []

for t in tmp:
        if t not in nodes:
                nodes.append(t)

node_sizes = {}
for n in nodes:
        node_sizes[n] = ' '.join(countsdic[n])

sizes = []

for v in node_sizes.values():
        x = int(v) * 10
        sizes.append(x)

g = nx.Graph()
#g.add_nodes_from(nodes)

g.add_edges_from(edges)

#for node in nodes:
#        if node in hybrids:
#                color = 'green'
#        if node not in hybrids:
#                color = 'blue'

pos=nx.graphviz_layout(g, prog='fdp')
nx.draw_networkx_nodes(g, pos, nodelist=[str(n) for n in nodes], node_color='b', node_size = sizes)
nx.draw_networkx_nodes(g, pos, nodelist=[str(n) for n in nodes if n in hybrids], node_color='g', node_size = sizes)
nx.draw_networkx_edges(g,pos)
#nxgraph(graph)

#for node in nodes:
#       if node in hybrids:
#               y.add_node(node, fillcolor='green')
#       if node not in hybrids:
#               g.add_node(node, fillcolor='blue')

A = nx.to_agraph(g)
A.layout(prog="fdp")
A.draw(inp + "2.png")

plt.figure(1,figsize=(2000,2000))
plt.savefig(out + ".png", dpi = 1000)
plt.show()

However, using the fdp format with agraph made everything black. I would still like to make the nodes specific colors if anyone can help with that. I also would like to keep the original shape and format of the graph, and simply change the node color, if anyone can still help with that. I will continue to work on this and post another answer if I figure it out. Thanks to anyone who looked at this post. (I could not post the updated image as was too large)