Vizualize distance matrix into graph

Question

For the following distance matrix:

∞, 1, 2
∞, ∞, 1
∞, ∞, ∞

I would need to visualise the following graph:
That's how it should look like

I tried with the following code:

import networkx as nx
import numpy as np
import string

dt = [('len', float)]
A = np.array([ (0, 1, None, 3, None),
               (2, 0, 4, 1, None),
               (5, None, 0, 3, None),
               (None, None, None, 0, None),
               (None, None, None, 2, 0),
               ])*10
A = A.view(dt)

G = nx.from_numpy_matrix(A)   

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('out.png', format='png', prog='neato')

but I cannot seem to input infinity (∞) to show that there is no connection. I tried with None, -1, and even ∞ but nothing seems to work right, so if anyone has any idea how I can visualise that distance matrix, please let me know.

Do you want to create the underlying unweighted directed graph? That means you would only create an edge for those entries in your distance matrix, if the value is exactly 1 — Sparky05, Jan 18 '22 at 07:23

score 0 · Accepted Answer · answered Jan 17 '22 at 16:23

It's not immediately obvious if this is what you are after, but one option is to use np.inf to denote the infinity. Below is a snippet where edges with value np.inf are removed, but whether this makes sense will depend on the context:

import networkx as nx
import numpy as np

A = np.array(
    [
        (0, 1, np.inf),
        (2, 0, 4),
        (5, np.inf, 0),
    ],
    dtype="float",
)

# if edge is np.inf replace with zero
A[A == np.inf] = 0

G = nx.from_numpy_matrix(A, create_using=nx.DiGraph)
G = nx.drawing.nx_agraph.to_agraph(G)
G.node_attr.update(color="red", style="filled")
G.edge_attr.update(color="blue", width="0.3")
G.draw("out.png", format="png", prog="neato")

Vizualize distance matrix into graph

1 Answers1