Drawing graph with 1200 nodes, and all nodes overlapped with each other

[Noob]

Hi all,

i have a weird issue when drawing a graph with about 1200 nodes.

I intend to draw a graph with multiple node colors and node shapes, and the code responsible for drawing my graph is as follows:

    

    import matplotlib.pyplot as plt    

    import networkx as nx 

    entire_graph = nx.DiGraph()

    # graph is being build based on retweet relationships.... some code truncated....

    ns = len(entire_graph)

    plt.figure(figsize=(100,100))    

    pos=nx.spring_layout(entire_graph)

    

    nx.draw_networkx_nodes(entire_graph,pos,

                           nodelist=list_of_nodes['yellow'],

                           node_color='#FFE303',

                           node_shape='o',

                           node_size=ns,

                       alpha=0.8)

    nx.draw_networkx_nodes(entire_graph,pos,

                           nodelist=list_of_nodes['blue'],

                           node_color='#0066CC',

                           node_shape='o',

                           node_size=ns,

                       alpha=0.8)

    nx.draw_networkx_nodes(entire_graph,pos,

                           nodelist=list_of_nodes['green'],

                           node_color='#00FF00',

                           node_shape='o',

                           node_size=ns,

                       alpha=0.8)

    nx.draw_networkx_nodes(entire_graph,pos,

                           nodelist=list_of_nodes['d'],

                           node_shape='d',

                           node_size=ns,

                       alpha=0.8)

    nx.draw_networkx_nodes(entire_graph,pos,

                           nodelist=list_of_nodes['p'],

                           node_shape='p',

                           node_size=ns,

                       alpha=0.8)

    nx.draw_networkx_nodes(entire_graph,pos,

                           nodelist=list_of_nodes['h'],

                           node_shape='h',

                           node_size=ns,

                       alpha=0.8)

    nx.draw_networkx_nodes(entire_graph,pos,

                           nodelist=list_of_nodes['8'],

                           node_shape='8',

                           node_size=ns,

                       alpha=0.8)

    # edges

    nx.draw_networkx_edges(entire_graph,pos)

    edgelist = []

    for _g in entire_graph:

        for k,v in enumerate(entire_graph[_g]):

            

            t = (_g, v)

            edgelist.append(t)

            

            

    file = "spring_layout.png"

    #nx.draw_networkx_nodes(g,pos,nodelist=[g],node_size=node_size_number,node_color='r')

    

    nx.draw_networkx_edges(entire_graph,pos,

                           edgelist=edgelist,

                           width=0.8,alpha=1)

    plt.axis('off')

    plt.savefig(file)

I've tried varying the node_size and figure size, and using the spring layout i end up with a drawing

where all nodes overlap with each other. ( see spring_layout.png )

I've tried using other layout such as circular layout, i end up with a diagram looking like circular.png

Any ideas/suggestions/advise for me?  I would prefer to use the spring layout if possible,

Thanks!

[Brian Keegan]

With anything larger than toy networks a few dozen nodes, I would recommend exporting the data to a dedicated network visualization package like Pajek, Gephi, or Cytoscape.

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Brian C. Keegan
Ph.D. Student - Media, Technology, & Society
School of Communication, Northwestern University

Science of Networks in Communities, Laboratory for Collaborative Technology

[gsal]

Can you just take the "pos" array and multiply it by some number?  That would increase the distance between all nodes...you may have to increase the size of the fig, but that can be done interactively in matplotlib.  Anyway, this would increase the distance between nodes without increasing the size of the nodes.