{"action":"created","issue":{"url":"https://api.github.com/repos/Becksteinlab/hop/issues/14","repository_url":"https://api.github.com/repos/Becksteinlab/hop","labels_url":"https://api.github.com/repos/Becksteinlab/hop/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/Becksteinlab/hop/issues/14/comments","events_url":"https://api.github.com/repos/Becksteinlab/hop/issues/14/events","html_url":"https://github.com/Becksteinlab/hop/issues/14","id":134418304,"number":14,"title":"visualization of hopping network","user":{"login":"orbeckst","id":237980,"avatar_url":"https://avatars.githubusercontent.com/u/237980?v=3","gravatar_id":"","url":"https://api.github.com/users/orbeckst","html_url":"https://github.com/orbeckst","followers_url":"https://api.github.com/users/orbeckst/followers","following_url":"https://api.github.com/users/orbeckst/following{/other_user}","gists_url":"https://api.github.com/users/orbeckst/gists{/gist_id}","starred_url":"https://api.github.com/users/orbeckst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/orbeckst/subscriptions","organizations_url":"https://api.github.com/users/orbeckst/orgs","repos_url":"https://api.github.com/users/orbeckst/repos","events_url":"https://api.github.com/users/orbeckst/events{/privacy}","received_events_url":"https://api.github.com/users/orbeckst/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-02-17T22:23:28Z","updated_at":"2016-02-24T14:57:54Z","closed_at":null,"body":"via @iorga:\r\n\r\nHow can we visualize the network encoded by the file **hopgraph.xgmml** ? I tried with Cytoscape, it recognizes the columns etc, but the drawing shows only one big rectangle.\r\n\r\nI also installed graphviz, but I'm not sure about how to use the modules, like \"dot\" for example. Is it correct to type\r\n```\r\ndot -Tpng -o x.png test.xgmml\r\n```\r\nThe result is :\r\n```\r\nWarning: test.xgmml: syntax error in line 1 near '>'\r\n```\r\nOr do I have to format the xgmml file into a specific format ?"},"comment":{"url":"https://api.github.com/repos/Becksteinlab/hop/issues/comments/188290969","html_url":"https://github.com/Becksteinlab/hop/issues/14#issuecomment-188290969","issue_url":"https://api.github.com/repos/Becksteinlab/hop/issues/14","id":188290969,"user":{"login":"ianWelland","id":17454708,"avatar_url":"https://avatars.githubusercontent.com/u/17454708?v=3","gravatar_id":"","url":"https://api.github.com/users/ianWelland","html_url":"https://github.com/ianWelland","followers_url":"https://api.github.com/users/ianWelland/followers","following_url":"https://api.github.com/users/ianWelland/following{/other_user}","gists_url":"https://api.github.com/users/ianWelland/gists{/gist_id}","starred_url":"https://api.github.com/users/ianWelland/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ianWelland/subscriptions","organizations_url":"https://api.github.com/users/ianWelland/orgs","repos_url":"https://api.github.com/users/ianWelland/repos","events_url":"https://api.github.com/users/ianWelland/events{/privacy}","received_events_url":"https://api.github.com/users/ianWelland/received_events","type":"User","site_admin":false},"created_at":"2016-02-24T14:57:54Z","updated_at":"2016-02-24T14:57:54Z","body":"Hi,\r\n\r\nThere are several strategies to visualize hop networks.\r\n\r\n1. Import networkx. Load the HoppingGraph. Filter the graph using the filter method. Then use:\r\nA=nx.to_agraph(hopgraph.filtered_graph)\r\nA.layout()\r\nA.draw('filename.png')\r\n\r\nA.layout() normally calls the 'neato' layout. These look much nicer than Cytoscape even for large graphs. You can change the layout and I think each layout has various nice properties.\r\n\r\n2. Use my tcl visualization tools. I believe my tcl visualization methods were merged with the master branch. \r\n\r\nWith your hopgraph, use h.write_tcl(filename='your_filename'). You can tweak the color of the edges and nodes, the size of the nodes, and also select subsets of nodes to highlight with a different color. There are some unfinished tools which try to color by weight but they don't produce very clear results.\r\n\r\n3. Use cytoscape.\r\n\r\nTo use cytoscape, you need to use the import tool. Then you need to change the layout of the graph, since otherwise it will 'helpfully' stack all the nodes on top of each other.\r\n\r\nBest,\r\nIan"}}