Plotting directed graphs in Python in a way that show all edges separately

问题

I'm using Python to simulate a process that takes place on directed graphs. I would like to produce an animation of this process.

The problem that I've run into is that most Python graph visualization libraries combine pairs of directed edges into a single edge. For example, NetworkX draws only two edges when displaying the following graph, whereas I would like to display each of the four edges separately:

import networkx as nx
import matplotlib.pyplot as plt 

G = nx.MultiDiGraph()

G.add_edges_from([
    (1, 2),
    (2, 3),
    (3, 2),
    (2, 1),
])

plt.figure(figsize=(8,8))
nx.draw(G)

I would like to display something like this, with each parallel edge drawn separately:

The question R reciprocal edges in igraph in R seems to deal with the same issue, but the solution there is for the R igraph library, not the Python one.

Is there an easy way to produce this style of plot using an existing Python graph visualization library? It would be a bonus if it could support multigraphs.

I'm open to solutions that invoke an external program to produce the images. I'd like to generate a whole series of animation frames, so the solution must be automated.

回答1:

The Graphviz tools appear to display distinct edges.

For example, giving this:

digraph G {
  A -> B;
  A -> B;
  A -> B;
  B -> C;

  B -> A;
  C -> B;
}

to dot produces:

Graphviz's input language is pretty simple so you can generate it on your own, though searching for "python graphviz" does turn up a couple of libraries including a graphviz module on PyPI.

Here's python that generates the above graph using the graphviz module:

from graphviz import Digraph

dot = Digraph()
dot.node('A', 'A')
dot.node('B', 'B')
dot.node('C', 'C')
dot.edges(['AB', 'AB', 'AB', 'BC', 'BA', 'CB'])

print(dot.source)
dot.render(file_name, view=True)

回答2:

Using NetworkX, a possible workaround which avoids file I/O and uses dot via pydot for layout is:

import networkx as nx
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
from io import BytesIO

g = nx.dodecahedral_graph()
d = nx.drawing.nx_pydot.to_pydot(g) # d is a pydot graph object, dot options can be easily set
# attributes get converted from networkx,
# use set methods to control dot attributes after creation

png_str = d.create_png()
sio = BytesIO() # file-like string, appropriate for imread below
sio.write(png_str)
sio.seek(0)

img = mpimg.imread(sio)
imgplot = plt.imshow(img)

for why seek(0) is needed, see How to create an image from a string in python

If within IPython (qt)console, then the above will print inline and a more direct approach is:

import networkx as nx
from IPython.display import Image

g = nx.dodecahedral_graph()
d = nx.drawing.nx_pydot.to_pydot(g)

png_str = d.create_png()
Image(data=png_str)

来源：https://stackoverflow.com/questions/10379448/plotting-directed-graphs-in-python-in-a-way-that-show-all-edges-separately

标签

python

graph-visualization