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Use of undirected graph in plot_msm_network

Open jeiros opened this issue 6 years ago • 4 comments

Is there a reason why an undirected graph is built from the transition matrix in the plot_msm_network function?

I've checked and the edges that are built when using an undirected graph do not match the entries of the transition matrix:

import networkx as nx
import numpy as np
tmat = np.array(
    [
        [0.8, 0.1, 0.1],
        [0.3, 0.6, 0.1],
        [0.0, 0.3, 0.7]
    ]
)
graph_di = nx.DiGraph(tmat)
graph_un = nx.Graph(tmat)
tot_un = 0
for v in graph_un.edge[0].values():
    tot_un += v['weight']
tot_di = 0
for v in graph_di.edge[0].values():
    tot_di += v['weight']
assert tot_di == tmat[0, :].sum()
assert tot_un == tmat[0, :].sum()

Traceback (most recent call last):
  File "/Users/je714/test_issue_tmat.py", line 19, in <module>
    assert tot_un == tmat[0, :].sum()
AssertionError
print(graph_di.edge)
{0: {0: {'weight': 0.8}, 1: {'weight': 0.1}, 2: {'weight': 0.1}},
 1: {0: {'weight': 0.3}, 1: {'weight': 0.6}, 2: {'weight': 0.1}},
 2: {1: {'weight': 0.3}, 2: {'weight': 0.7}}}
print(graph_un.edge)
{0: {0: {'weight': 0.8}, 1: {'weight': 0.3}, 2: {'weight': 0.1}},
 1: {0: {'weight': 0.3}, 1: {'weight': 0.6}, 2: {'weight': 0.3}},
 2: {0: {'weight': 0.1}, 1: {'weight': 0.3}, 2: {'weight': 0.7}}}

Also, as a side question: is there a way to hide the edges below a particular weight? When there are too many connections, the resulting plot is really crowded and is a bit confusing to look at.

jeiros avatar Sep 26 '17 09:09 jeiros