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.
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
If you want to generate a dot file, you can do so using
G.draw('/tmp/out.dot', format='dot', prog='neato')
which yields
strict graph {
graph [bb="0,0,226.19,339.42"];
node [color=red,
label="\N",
style=filled
];
edge [color=blue,
width=2.0
];
B [height=0.5,
pos="27,157.41",
width=0.75];
D [height=0.5,
pos="69,303.6",
width=0.75];
B -- D [len=2.0,
pos="32.15,175.34 40.211,203.4 55.721,257.38 63.808,285.53"];
A [height=0.5,
pos="199.19,18",
width=0.75];
B -- A [len=3.0,
pos="44.458,143.28 77.546,116.49 149.02,58.622 181.94,31.965"];
C [height=0.5,
pos="140.12,321.42",
width=0.75];
B -- C [len=9.0,
pos="38.469,174.04 60.15,205.48 106.92,273.28 128.62,304.75"];
D -- A [len=7.0,
pos="76.948,286.17 100.19,235.18 167.86,86.729 191.18,35.571"];
D -- C [len=1.0,
pos="94.274,309.94 100.82,311.58 107.88,313.34 114.45,314.99"];
A -- C [len=4.0,
pos="195.67,36.072 185.17,90.039 154.1,249.6 143.62,303.45"];
}
The png
file could then be generated using the graphviz
neato
program:
neato -Tpng -o /tmp/out.png /tmp/out.dot