Networkx和graphviz布局将节点放置在同一位置

Question

I'm using the networkx library to do some work with graphs and using matplotlib for visualising.

The problem I'm having is that the nodes are getting placed over each other. I am using my own classes for the nodes - a simplified, runnable version shown here:

import matplotlib
matplotlib.use('TKAgg')
import matplotlib.pyplot as plt
import networkx as nx

class MyCustomNode(object):
    def __init__(self, value):
    self.value = value

def __str__(self):
    return "val: " + self.value


graph = nx.Graph()
graph.add_edge(MyCustomNode('a'), MyCustomNode('b'))

labels = {}
for node in graph.nodes():
    labels[node] = str(node)

pos = nx.graphviz_layout(graph)
nx.draw(graph, pos, node_color='red', node_size=3000)
nx.draw_networkx_labels(graph, pos, labels, font_size=8, font_color='white')
plt.show()

What I've found is that the behaviour seems to what gets returned in the __str__ method. If I change the __str__ method to something where the starting is unique, it lays out as expected:

def __str__(self):
    return self.value 

Can't tell if this is the expected behaviour, or I'm doing something wrong, or this is a bug. Advice appreciated! :)

Answer 1

Although I can't find an authoritative reference at the moment, here's what's going on:

Graphviz has some restrictions on what characters can appear in node names. Among the characters it cannot handle is : . So when everything was passed to graphviz, I believe it interpreted it as a single node whose name was just val (I may be wrong).

Then when networkx got the positions back from graphviz, it resulted in all the nodes being put in the same place.

So your simplest option is to remove the colon.