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I want to make a network graph which shows the distribution of our documents in our folder structure.

I have the nodefile, edgefile and gephi graph file in this location: https://1drv.ms/f/s!AuVfRBdVHkO7hgs5K9r9f7jBBAUH

What I do is: Run the algorithm ForceAtlas2 with scaling 10-20, dissuade hub marked and prevent overlap marked, all other standard setting.

What I get is a graph with groups radial/spherical distributed. However, what I want is a tree directed network graph. Anyone know how I can adjust Gephi to make this? Thanks!

PDG
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2 Answers2

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I just found a solution. I tested the file format as shown on the Yed site "import excel file" page http://yed.yworks.com/support/manual/import_excel.html

This gave me the Yed import dialog (took a life time to figure out that it's a pop up menu and not selectable through the standard menu) Anyway, it worked and I've adjusted the test files with the data prepared for the Gehpi. This was pretty easy, I could used the source target ID's etc. Just copy paste.

I load it into Yed and used some directed and radial clustering algorithms on it. Works fine!

Below you can find the excel node/edge file used to import in Yed and the graph file you can open with Yed to see the final radial result.

https://1drv.ms/f/s!AuVfRBdVHkO7hg6DExK_eVkm5_mR

Only thing to figure out is how to combine the weight (which represents the number of documents) with the node size.

PDG
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Unfortunately, as of version 0.9.0, Gephi no longer supports hierarchical graphs. Maybe try using a previous version?

Other alternatives involve more complex software, such as Graphviz, but you need a .dot file instead of your .csv. I looked all over, but could not find an easy-to-use csv to dot converter.

You could try looking at d3-hierarchy, a node.js program, but then again you need to use the not-so-user-friendly npm. If you look at the link, it looks like it can produce the kind of diagram you're looking for.

MikaelF
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  • Thank you for your answer. Like you said, I also tried to look for alternatives. For example Yed, I'm quit familiar with it. It can take in the export general graph files from Gephi, however when I tried that it gave a messed up result. If you know of a place where it's explained the import format requirements for Yed, that would also be helpful, I can't find it. Perhaps I can produce a dendogram with R. But like you pointed out, unfortunately there is no standard file and format that is used between all those programs, except for the general graph files but result is not guaranteed. – PDG Feb 03 '17 at 06:25