Networkx Random Geometric Graph limit nodes within radius r

graph, networkx, python

Solution

You could use a dict comprehension such as

p = {node:length for node, length in nx.single_source_shortest_path_length(G,ncenter).items()
     if length < 5}

to limit the dict to those nodes whose distance from `ncenter` is < 5.

For Python2.6 or older, you could use

p = dict((node, length) for node, length in nx.single_source_shortest_path_length(G,ncenter).items()
     if length < 5)

You could also replace

dmin =1
ncenter =0
for n in pos:
    x,y = pos[n]
    d = (x-0.5)**2+(y-0.5)**2
    if d<dmin:
        ncenter = n
        dmin = d

with a one-liner:

ncenter, _ = min(pos.items(), key = lambda (node, (x,y)): (x-0.5)**2+(y-0.5)**2)

To draw only those nodes whose distance from `ncenter` is < 5, define the subgraph:

H = G.subgraph(p.keys())    
nx.draw_networkx_edges(H, pos, alpha = 0.4)
nx.draw_networkx_nodes(H, pos, node_size = 80, node_color = node_color,
                       cmap = plt.get_cmap('Reds_r'))

import networkx as nx
import matplotlib.pyplot as plt
G = nx.random_geometric_graph(1000, 0.1)

# position is stored as node attribute data for random_geometric_graph
pos = nx.get_node_attributes(G, 'pos')

# find node near center (0.5,0.5)
ncenter, _ = min(pos.items(), key = lambda (node, (x, y)): (x-0.5)**2+(y-0.5)**2)

# color by path length from node near center
p = {node:length
     for node, length in nx.single_source_shortest_path_length(G, ncenter).items()
     if length < 5}

plt.figure(figsize = (8, 8))
node_color = p.values()
H = G.subgraph(p.keys())    
nx.draw_networkx_edges(H, pos, alpha = 0.4)
nx.draw_networkx_nodes(H, pos, node_size = 80, node_color = node_color,
                       cmap = plt.get_cmap('Reds_r'))

plt.xlim(-0.05, 1.05)
plt.ylim(-0.05, 1.05)
plt.axis('off')
plt.savefig('random_geometric_graph.png')
plt.show()

Problem

Original source