I am trying to display a tree graph of my class hierarchy using networkx.
I have it all graphed correctly, and it displays fine. But as a circular graph with crossing edges, it is a pure hierarchy, and it seems I ought to be able to display it as a tree.
I have googled this extensively, and every solution offered involves using pygraphviz
... but PyGraphviz does not work with Python 3 (documentation from the pygraphviz site).
Has anyone been able to get a tree graph display in Python 3?
[scroll down a bit to see what kind of output the code produces]
edit (7 Nov 2019) I've put a more refined version of this into a package I've been writing: https://epidemicsonnetworks.readthedocs.io/en/latest/_modules/EoN/auxiliary.html#hierarchy_pos. The main difference between the code here and the version there is that the code here gives all children of a given node the same horizontal space, while the code following that link also considers how many descendants a node has when deciding how much space to allocate it.
edit (19 Jan 2019) I have updated the code to be more robust: It now works for directed and undirected graphs without any modification, no longer requires the user to specify the root, and it tests that the graph is a tree before it runs (without the test it would have infinite recursion - see user2479115's answer for a way to handle non-trees).
edit (27 Aug 2018) If you want to create a plot with the nodes appearing as rings around the root node, the code right at the bottom shows a simple modification to do this
edit (17 Sept 2017) I believe the trouble with pygraphviz that OP was having should be fixed by now. So pygraphviz is likely to be a better solution that what I've got below.
Here is a simple recursive program to define the positions. The recursion happens in _hierarchy_pos
, which is called by hierarchy_pos
. The main role of hierarcy_pos
is to do a bit of testing to make sure the graph is appropriate before entering the recursion:
import networkx as nx
import random
def hierarchy_pos(G, root=None, width=1., vert_gap = 0.2, vert_loc = 0, xcenter = 0.5):
'''
From Joel's answer at https://stackoverflow.com/a/29597209/2966723.
Licensed under Creative Commons Attribution-Share Alike
If the graph is a tree this will return the positions to plot this in a
hierarchical layout.
G: the graph (must be a tree)
root: the root node of current branch
- if the tree is directed and this is not given,
the root will be found and used
- if the tree is directed and this is given, then
the positions will be just for the descendants of this node.
- if the tree is undirected and not given,
then a random choice will be used.
width: horizontal space allocated for this branch - avoids overlap with other branches
vert_gap: gap between levels of hierarchy
vert_loc: vertical location of root
xcenter: horizontal location of root
'''
if not nx.is_tree(G):
raise TypeError('cannot use hierarchy_pos on a graph that is not a tree')
if root is None:
if isinstance(G, nx.DiGraph):
root = next(iter(nx.topological_sort(G))) #allows back compatibility with nx version 1.11
else:
root = random.choice(list(G.nodes))
def _hierarchy_pos(G, root, width=1., vert_gap = 0.2, vert_loc = 0, xcenter = 0.5, pos = None, parent = None):
'''
see hierarchy_pos docstring for most arguments
pos: a dict saying where all nodes go if they have been assigned
parent: parent of this branch. - only affects it if non-directed
'''
if pos is None:
pos = {root:(xcenter,vert_loc)}
else:
pos[root] = (xcenter, vert_loc)
children = list(G.neighbors(root))
if not isinstance(G, nx.DiGraph) and parent is not None:
children.remove(parent)
if len(children)!=0:
dx = width/len(children)
nextx = xcenter - width/2 - dx/2
for child in children:
nextx += dx
pos = _hierarchy_pos(G,child, width = dx, vert_gap = vert_gap,
vert_loc = vert_loc-vert_gap, xcenter=nextx,
pos=pos, parent = root)
return pos
return _hierarchy_pos(G, root, width, vert_gap, vert_loc, xcenter)
and an example usage:
import matplotlib.pyplot as plt
import networkx as nx
G=nx.Graph()
G.add_edges_from([(1,2), (1,3), (1,4), (2,5), (2,6), (2,7), (3,8), (3,9), (4,10),
(5,11), (5,12), (6,13)])
pos = hierarchy_pos(G,1)
nx.draw(G, pos=pos, with_labels=True)
plt.savefig('hierarchy.png')
Ideally this should rescale the horizontal separation based on how wide things will be beneath it. I'm not attempting that but this version does: https://epidemicsonnetworks.readthedocs.io/en/latest/_modules/EoN/auxiliary.html#hierarchy_pos
Radial expansion
Let's say you want the plot to look like:
Here's the code for that:
pos = hierarchy_pos(G, 0, width = 2*math.pi, xcenter=0)
new_pos = {u:(r*math.cos(theta),r*math.sin(theta)) for u, (theta, r) in pos.items()}
nx.draw(G, pos=new_pos, node_size = 50)
nx.draw_networkx_nodes(G, pos=new_pos, nodelist = [0], node_color = 'blue', node_size = 200)
edit - thanks to Deepak Saini for noting an error that used to appear in directed graphs