How to change the color of subgraph using pyvis?

Question

I want to visualize the graph using pyviz. I'm working on the code to extract a subgraph from a graph.

import networkx as nx
import numpy as np
import matplotlib.pyplot as plt

def RWS(G, vs, r=0.5, S=4):
    #initialize subgraph
    Gk = nx.DiGraph()
    #initialize nodes 
    Vk = [] 

    #add vs to Gk
    Gk.add_node(vs) 
    Vk.append(vs)

    while len(Vk) < S:
        #get neighbor nodes set of Vk (step 4) (Also appending j just for the purpose of adding edge)
        NS = [(n, j) for j in Vk for n in G.neighbors(j) if n not in Vk]
        print("{} {} {} {}".format('length of NS is', len(NS), 'and vs =', vs))
        # randomly select r of nodes in NS, add them into the Vk
        if not len(NS) == 0:
            for node, j in NS:
                if np.random.uniform() < r:
                    Vk.append(node)
                    Gk.add_edge(j, node)
                    if len(Vk) == S or len(NS) < S:
                        break
        else:
            break
    return Gk


if __name__ == '__main__':

    m = np.matrix([
    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 
    [1, 0, 0, 0, 0, 1, 0, 0, 0, 0], 
    [0, 1, 0, 0, 0, 0, 0, 0, 0, 0], 
    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 
    [0, 0, 0, 1, 0, 0, 0, 0, 0, 0], 
    [0, 0, 0, 0, 1, 0, 1, 1, 0, 0], 
    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 
    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 
    [0, 0, 0, 0, 0, 0, 0, 1, 0, 0], 
    [0, 0, 0, 0, 0, 0, 0, 1, 0, 0]])

    # G = nx.from_numpy_matrix(m, create_using=nx.MultiDiGraph())
    G =  nx.from_numpy_matrix(m, create_using=nx.DiGraph)
    #expansion ratio
    r  = 0.5
    #subgraph size
    S  = 4
    # randomly select the node from G
    vs = np.random.randint(0, G.size()) 
    print(vs)

    Gk = RWS(G, vs, r, S)


    # VISUALIZATION
    pos = nx.spring_layout(G)
    nx.draw_networkx_nodes(G, pos)
    nx.draw_networkx_nodes(G, pos, nodelist=list(Gk.nodes()), node_color='r')
    nx.draw_networkx_labels(G, pos)
    nx.draw_networkx_edges(G, pos, edge_color='b', width=0.5)
    nx.draw_networkx_edges(G, pos, edgelist=list(Gk.edges()), edge_color='g', width=1, arrowstyle='->')

    plt.axis('off')
    plt.show()

Here I have the graph in networkx format, and extract the subgraph from it, then visualize with networkx. To make it easier to see, subgraph is colored green. However, this visualization does not work well for large scaled graph.

So I want to recreate the visualization of this using pyvis. Can someone help me tto complete this?

Answer 1

In order to visualize this graph in pyvis, you can write the following function:

from pyvis.network import Network


def visualize(G, SG):
    N = Network(height='100%', width='100%', bgcolor='#222222', font_color='white', directed=True)
    # uncomment the following if the graph is large
    # N.barnes_hut(spring_strength=0.006)

    for n in G:
        if n in SG:  # if the node is part of the sub-graph
            color = 'green'
        else:
            color = 'red'
        N.add_node(n, label=n, color=color)

    for e in G.edges:
        if e in SG.edges:  # if the edge is part of sub-graph
            color = 'green'
            width = 2
        else:
            color = 'red'
            width = 0.5
        N.add_edge(int(e[0]), int(e[1]), color=color, width=width)

    N.write_html('subgraph.html')  # save a html file in current dir

Make sure that the graph and the sub-graph are both of the same type:

G = nx.from_numpy_matrix(m, create_using=nx.MultiDiGraph())
Gk = nx.MultiDiGraph()  # changed the graph type to MultiDiGraph

and finally you will have:

# VISUALIZATION
visualize(G, Gk)