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POBig Graph visualization on a webpage : networkx, vivagraph
 

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  1. POBig Graph visualization on a webpage : networkx, vivagraph
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    <p>I have a graph of about 5000 nodes and 5000 links, that i can visualize in Chrome thanks to <a href="https://github.com/anvaka/VivaGraphJS" rel="noreferrer">the vivagraph javascript library</a> (webgl is faster than svg - in d3 for example). </p> <p>My workflow is :</p> <ul> <li>Building with the <a href="http://networkx.github.io/" rel="noreferrer">networkx</a> python library and output the result as a json file.</li> <li>Load the json and construct the graph with <a href="https://github.com/anvaka/VivaGraphJS" rel="noreferrer">the vivagraph javascript library</a>.</li> <li>Nodes positions are computed by the js library</li> </ul> <p>The problem is that it takes time to render the layout with well positionned nodes.</p> <p>My approach is to pre-compute the nodes position in <a href="http://networkx.github.io/" rel="noreferrer">networkx</a> for example. The really good point on this approach is that it minimize client work on the browser. But i can't achieve good positions on the webpage. I need help on this step.</p> <p>The relevant python code for the node position computation is :</p> <pre><code> ## positionning try: # Position nodes using Fruchterman-Reingold force-directed algorithm. pos=nx.spring_layout(G) for k,v in pos.iteritems(): # scaling tentative # from small float like 0.5555 to higher values # casting to int because precision is not important pos[k] = [ int(i*1000) for i in v.tolist() ] except Exception, e: print "positionning failed" raise ## setting positions try: # set position of nodes as a node attribute # that will be used with the js library nx.set_node_attributes(G,'pos', pos) except Exception, e: print "getting positions failed" raise e # output all the stuff d = json_graph.node_link_data(G) with open(args.output,'w') as f: json.dump(d,f) </code></pre> <p>Then in my page, in javascript :</p> <pre><code>/*global Viva*/ function graph(file){ var file = file; $.getJSON(file, function(data) { var graphGenerator = Viva.Graph.generator(); graph = Viva.Graph.graph(); # building the graph with the json data : data.nodes.forEach(function(n,i) { var node = graph.addNode(n.id,{d: n.d}); # node position is defined in the json element attribute 'pos' node.position = { x : n.pos[0], y : n.pos[1] }; }) # adding links between nodes data.links.forEach(function(l,i) { graph.addLink(data.nodes[l.source].id, data.nodes[l.target].id); }) var max_link = 55 var min_link = 1 var colors = d3.scale.linear().domain([min_link,max_link]).range(['#F0F0F0','#252525']); var layout = Viva.Graph.Layout.forceDirected(graph, { springLength : 80, springCoeff : 0.0008, dragCoeff : 0.001, gravity : -5.0, theta : 0.8 }); var graphics = Viva.Graph.View.webglGraphics(); graphics .node(function(node){ # color and size of nodes color = colors(node.links.length) if(node.id == "root"){ // pin node on canvas, so no position update node.isPinned = true; size = 60; } else { size = 20+(7-node.id.length)*(7-node.id.length); } return Viva.Graph.View.webglSquare(size,color); }) .link(function(link) { # color on links fromId = link.fromId; toId = link.toId; if(toId == "root" || fromId == "root"){ return Viva.Graph.View.webglLine("#252525"); } else { if( fromId[0] == toId[0]){ linkcolor = linkcolors(fromId[0]) return Viva.Graph.View.webglLine(linkcolor); } else { linkcolor = averageRGB(linkcolors(fromId[0]),linkcolors(toId[0])) return Viva.Graph.View.webglLine('#'+linkcolor); } } }); renderer = Viva.Graph.View.renderer(graph, { layout : layout, graphics : graphics, enableBlending: false, renderLinks : true, prerender : true }); renderer.run(); }); } </code></pre> <p>I am now trying <a href="https://gephi.org" rel="noreferrer">Gephi</a>, but i don't want to use the <a href="https://gephi.org/toolkit/" rel="noreferrer">gephi toolkit</a> as i am not used to java.</p> <p>If somebody got some hints on this, please avoid me hundred of trials and maybe failure ;)</p>
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    1. COHi, have you found anything useful for your question?
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    2. COHi, in fact i switched to another kind of solution : i use d3.js to display a static graph in svg, then i save the (big) svg and render it in png with a big resolution. Then i get tiles of it with gda2tiles.py and use leafletJS to display it ala google maps !
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    3. COWow that's a lot of work! Thanks for the sharing mate :)
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