sol - 1 month ago 20
Python Question

# Drawing a graph or a network from a distance matrix?

I'm trying to plot/sketch (matplotlib or other python library) a 2D network of a big distance matrix where distances would be the edges of the sketched network and the line and column its nodes.

``````DistMatrix =
[       'a',   'b',     'c',    'd'],
['a',   0,      0.3,    0.4,    0.7],
['b',   0.3,    0,      0.9,    0.2],
['c',   0.4,    0.9,    0,      0.1],
['d',   0.7,    0.2,    0.1,    0] ]
``````

I'm searching to sketch/plot the 2d network from such (bigger: thousand of columns and lines) distance matrix: node 'a' is linked to node 'b' by an edge depth of 0.3, nodes 'c' and 'd' would be tied by an edge depth of 0.1.
What are the tools/libraries I can used (distance matrix can be converted into numpy matrix) to get the sketch/graphical projection of such network? (pandas, matplotlib, igraph,...?) and some leads to do that quickly (I would not define my self Tkinter function to do that ;-) ) ?

The graphviz program `neato` tries to respect edge lengths. doug shows a way to harness `neato` using networkx like this:

``````import networkx as nx
import numpy as np
import string

dt = [('len', float)]
A = np.array([(0, 0.3, 0.4, 0.7),
(0.3, 0, 0.9, 0.2),
(0.4, 0.9, 0, 0.1),
(0.7, 0.2, 0.1, 0)
])*10
A = A.view(dt)

G = nx.from_numpy_matrix(A)
G = nx.relabel_nodes(G, dict(zip(range(len(G.nodes())),string.ascii_uppercase)))

G = nx.drawing.nx_agraph.to_agraph(G)

G.node_attr.update(color="red", style="filled")
G.edge_attr.update(color="blue", width="2.0")

G.draw('/tmp/out.png', format='png', prog='neato')
``````

yields