Group Nodes Together In Networkx

I have a visualization problem involving a graph. I have N nodes, which belong to say some M networks. The nodes can have inter-network edges (within the same network) and intra-ne

Solution 1:

To get better nodes layout, I start with using circular layout (replacing your spring-layout). Then I move each group of the nodes to their new locations along perimeter of a bigger circle.

# --- Begin_myhack ---# All this code should replace original `pos=nx.spring_layout(graph)`import numpy as np
pos = nx.circular_layout(graph)   # replaces your original pos=...# prep center points (along circle perimeter) for the clusters
angs = np.linspace(0, 2*np.pi, 1+len(colors))
repos = []
rad = 3.5# radius of circlefor ea in angs:
    if ea > 0:
        #print(rad*np.cos(ea), rad*np.sin(ea))  # location of each cluster
        repos.append(np.array([rad*np.cos(ea), rad*np.sin(ea)]))
for ea in pos.keys():
    #color = 'black'
    posx = 0if ea in nodes_by_color['green']:
        #color = 'green'
        posx = 0elif ea in nodes_by_color['royalblue']:
        #color = 'royalblue'
        posx = 1elif ea in nodes_by_color['red']:
        #color = 'red'
        posx = 2elif ea in nodes_by_color['orange']:
        #color = 'orange'
        posx = 3elif ea in nodes_by_color['cyan']:
        #color = 'cyan'
        posx = 4else:
        pass#print(ea, pos[ea], pos[ea]+repos[posx], color, posx)
    pos[ea] += repos[posx]
# --- End_myhack ---

The output plot will be similar to this:

EDIT

Usually, no particular layout is best in all situations. So, I offer the second solution which uses concentric circles to separate individual groups of the nodes. Here are the relevant code and its sample output.

# --- Begin_my_hack ---# All this code should replace original `pos=nx.spring_layout(graph)`import numpy as np
pos = nx.circular_layout(graph)
radii = [7,15,30,45,60]  # for concentric circlesfor ea in pos.keys():
    new_r = 1if ea in nodes_by_color['green']:
        new_r = radii[0]
    elif ea in nodes_by_color['royalblue']:
        new_r = radii[1]
    elif ea in nodes_by_color['red']:
        new_r = radii[2]
    elif ea in nodes_by_color['orange']:
        new_r = radii[3]
    elif ea in nodes_by_color['cyan']:
        new_r = radii[4]
    else:
        pass
    pos[ea] *= new_r   # reposition nodes as concentric circles# --- End_my_hack ---