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     Graph plots in Lightning

Setup

In [1]:
import os
from lightning import Lightning

from numpy import random, asarray, argmin
from colorsys import hsv_to_rgb
import networkx as nx

Connect to server

In [2]:
lgn = Lightning(ipython=True, host='http://public.lightning-viz.org')
Lightning initialized
Connected to server at http://public.lightning-viz.org

Random spatial graphs

Spatial graphs have nodes with fixed spatial positions, and links between them.
They are useful for spatial network data, where position has meaning (unlike force-directed graphs, where position is used dynamically during rendering).
First we'll generate a random geometric graph using networkx and plot with basic styling.
The random geometric graph places links between nodes with probability that depends on their spatial distance.

In [3]:
G = nx.random_geometric_graph(100, 0.2)
pos = asarray(nx.get_node_attributes(G, 'pos').values())
mat = nx.adjacency_matrix(G).todense()
In [4]:
lgn.graph(pos[:,0], pos[:,1], mat)
Out[4]:

We can add a color to each node. Here we color the same graph based on distance from the origin.

In [5]:
dists = [(x - 0.5)**2 + (y - 0.5)**2 for x, y in pos]
lgn.graph(pos[:,0], pos[:,1], mat, values=dists, colormap='Greens')
Out[5]:

As with other plots, we can also color using group labels.
Here we assign a label to each point based on the shortest path from it to the center.

In [6]:
center = argmin(dists)
p = nx.single_source_shortest_path_length(G, center)
xy = asarray([pos[i,:] for i in p.keys()])
g = p.values()
lgn.graph(xy[:,0], xy[:,1], mat, group=g)
Out[6]:

Edge bundling

Graphs with many edges can become hard to visualize (due to hairballs).
Lightning helps with this by letting you click on points and see only the links to that node. Try it!

In [7]:
G = nx.random_geometric_graph(50, 0.5)
pos = asarray(nx.get_node_attributes(G, 'pos').values())
dists = [(x - 0.5)**2 + (y - 0.5)**2 for x, y in pos]
mat = nx.adjacency_matrix(G).todense()
In [8]:
lgn.graph(pos[:,0], pos[:,1], mat)
Out[8]:

Another option is to bundle edges together using an algorithm by Holton and Van Wijk, emphasizing large tracts. See this link for the implementaiton.
As with the unbundled version, you can click on points to highlight links.

In [9]:
lgn.graphbundled(pos[:,0], pos[:,1], mat)
Out[9]: