Gephi forums

Re: Graphviz layout plugin

2012-12-21T01:59:42+01:00

It loads the graph information directly out of the graph that Gephi currently has. So, no: you shouldn't need to load stuff in as dot format.

Can you post an example gexf that shows the problem?

Thanks,
Gary

Statistics:Posted by chunkyks — 21 Dec 2012 01:59

Re: Graphviz layout plugin

2012-12-20T06:43:00+01:00

Yo,

Does your graph information have to be in the DOT file format to use the GraphViz plugin?

When I load a gexf or gml file into gephi, and try to use a GraphViz plugin, it doesn't work. But, when I downloaded the blueprint example DOT http://icculus.org/~chunky/stuff/gephi_ ... /graph.dotfile.. it worked like a charm.

If the plugin only does work in the DOT format, is there any way to convert a file Gephi exports into that format? Thanks so much brahs! zzz

Statistics:Posted by WeezyF — 20 Dec 2012 06:43

Re: Graphviz layout plugin

2012-02-21T17:52:55+01:00

By default, it just tries to run "dot", which presumes it'll be in your PATH somewhere. Perhaps OSX binaries don't get /usr/local/bin in their PATH [which(1) is probably working for you if it's set by a script that runs when you open your terminal].

Try manually changing the setting for "dot path" in the gui component to give the full path "/usr/local/bin/dot", or just put a symlink to that in /usr/bin or something?

Thanks,
Gary

Statistics:Posted by chunkyks — 21 Feb 2012 17:52

Re: Graphviz layout plugin

2012-02-09T23:50:09+01:00

Where does gephi search for the dot executable on Mac (Lion 10.7.3)?
I can launch it from command line and it is in my path:

dn5205as:local cengel$ which dot
/usr/local/bin/dot

but Gephi tells me "cannot run program "dot" error=2 no such file or directory".

Statistics:Posted by cengel — 09 Feb 2012 23:50

Re: Graphviz layout plugin

2012-01-18T20:41:29+01:00

1. What is the best layout for a gv file that has 17444 nodes and 18068 edges

Dunno. Suck it and see. I've had varying success with different layouts for different graphs. I find graphviz to be really slow for large graphs.

Don't forget that gephi has a lot of really good layout plugins in the box, too.

2. What is gephi way of doing Graphivs ccomps - command line ccomps -zX# -1000

Currently, there is none. I've never used or heard of it, so I didn't think to include it in my code.

3. Why will the Graphviz Plugin not find my installed Graphviz

Because it's not in your path. Either add the full path to the "dot" binary to your path, or edit the "dot binary" option in the graphviz layout to include the full path, plus executable, to dot.

I'm assuming you're on windows, so best bet for adding it to the path is to hit windows-break, go into advanced system configuration settings, and edit your PATH under "environment variables".

FWIW: http://icculus.org/~chunky/stuff/gephi_graphviz/

Gary (-;

Statistics:Posted by chunkyks — 18 Jan 2012 20:41

Re: Graphviz layout plugin

2012-01-02T00:55:36+01:00

Hi

Couple of questions:

I have been using Graphviz to visualize Twitter Stream files
and it has been doing a great job for simple coloring.

Today I came across Gephi and really like how easy and smooth it works.
Ran through the Les Miserables tutorial without a hitch beside mine being flipped
horizontally to the tutorial. No big deal.

Now the questions:
1. What is the best layout for a gv file that has 17444 nodes and 18068 edges
2. What is gephi way of doing Graphivs ccomps - command line ccomps -zX# -1000
3. Why will the Graphviz Plugin not find my installed Graphviz

Thanks

Harry Osoff

Statistics:Posted by finestjava — 02 Jan 2012 00:55

Re: Graphviz layout plugin

2011-10-31T17:45:01+01:00

Awesome, thank-you!

Gary

Statistics:Posted by chunkyks — 31 Oct 2011 17:45

Re: Graphviz layout plugin

2011-10-31T04:43:17+01:00

All right, it's now published!

Statistics:Posted by admin — 31 Oct 2011 04:43

Re: Graphviz layout plugin

2011-10-31T00:19:49+01:00

OK, I put in a helpful error message if the process can't be launched . Plugin is in the same place as before

Gary

Statistics:Posted by chunkyks — 31 Oct 2011 00:19

Re: Graphviz layout plugin

2011-10-29T22:10:30+01:00

Yeah, that's a good idea, and was already on my list of stuff to finish.

I mailed the plugins mailing list, but no answer yet; whats the correct way to report an error to the user?

Should I just do a JOptionPane, or is there a better process provided by netbeans or gephi?

Gary

Statistics:Posted by chunkyks — 29 Oct 2011 22:10

Re: Graphviz layout plugin

2011-10-29T20:29:09+01:00

Is there any way for the plugin to check if Graphviz in installed, and warn the user if it's not the case?

Statistics:Posted by admin — 29 Oct 2011 20:29

Re: Graphviz layout plugin

2011-10-27T08:15:36+01:00

I tried looking, but couldn't find a really good way to embed binaries in the jar that would work for all platforms, always.

Currently I just recommend that people install graphviz separately. That has the added benefit that folks can update their own install of graphviz faster than I can push updates. It sounds like a bit of a cop-out, but I have many negative experiences of developers "helpfully" bundling a specific version of something with their software, and then causing problems down the line.

Perhaps I'll look at embedding a binary just for Windows; I'm not sure what it needs, but I imagine windows users will be the ones least likely to have an easy path to getting dot installed. What do you think?

Gary (-;

Statistics:Posted by chunkyks — 27 Oct 2011 08:15

Re: Graphviz layout plugin

2011-10-27T07:23:46+01:00

Nice job! But I can't validate your plug-in as it's not out of the box. I got this exception (Graphviz not installed, windows 7):

java.io.IOException: CreateProcess error=2, Le fichier spécifié est introuvable
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.(ProcessImpl.java:81)
at java.lang.ProcessImpl.start(ProcessImpl.java:30)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
Caused: java.io.IOException: Cannot run program "dot": CreateProcess error=2, Le fichier spécifié est introuvable
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
[catch] at org.icculus.chunky.gephigraphviz.GraphvizLayout.goAlgo(GraphvizLayout.java:105)
at org.gephi.layout.LayoutControllerImpl$LayoutRun.run(LayoutControllerImpl.java:178)
at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:251)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)

Can you find a solution to embed the application?

Statistics:Posted by admin — 27 Oct 2011 07:23

Re: Graphviz layout plugin

2011-10-26T15:38:07+01:00

Cool ! I appreciate that you did it by yourself and contribute to the Gephi project !

Statistics:Posted by jacomyma — 26 Oct 2011 15:38

Graphviz layout plugin

2011-10-25T22:35:46+01:00

TLDR, plugin: http://icculus.org/~chunky/stuff/gephi_ ... aphviz.nbm

I have a bunch of graphs that graphviz does a great job of laying out.

I submitted a blueprint requesting a graphviz plugin, but I went ahead and wrote it myself. Also, all the cool kids bring code to the table

http://icculus.org/~chunky/stuff/gephi_graphviz/

Contained on that page is the source code, the .nbm plugin, and an example graph that dot does a good job of laying out [in this case, it's from a genetic algorithm I'm working on, showing ancestry]

Please feel free to try it and lemme know how it goes. This seemed like a really quick and easy way to bring a whole bunch of neat layout engines to Gephi.

Have fun,
Gary (-;

Statistics:Posted by chunkyks — 25 Oct 2011 22:35