sol - 7 months ago 105

Python Question

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 ;-) ) ?

thanks for your incoming answers.

Answer

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