Gephi

[geeklight01]

What are (all) the exportation steps in DNA to successfully import my network in GEPHI? Thanks!!

[leifeld]

Export to CSV file, then import the CSV file in Gephi. I will try to implement Gephi's GFX format when I get the chance over the next couple weeks. Alternatively, you may consider using visone.

[suncz01]

Have you already implemented the Gephi's format .graphml? Thank you!

[PhiBu91]

First things fist: I'm not an expert in coding. Now: I try to import a .graphml file exported from DNA in Gephi, but always get the same error (sf. screenshot). Whats the reason for that? Can anyone help?

[leifeld]

DNA exports the visone dialect of graphml. It's basically graphml with additional information for coloring the nodes and edges and similar visual information embedded straight into the file. You can open the exported graphml file in any text editor or XML viewer or browser to see how the data are structured and that there are several add-on definitions for visone. The basic graphml specification (i.e., without the visone additions) is described here.

The error messages mean that Gephi does not recognize these visone-specific additions. I am not sure if this is because there is some omission in the graphml files DNA exports or if this is because Gephi does not recognize additions to the graphml format, such as the ones used by visone. I guess a first diagnostic test could be to save some other graphml file from visone, perhaps a basic toy example with a couple of nodes and edges, and compare it to the graphml file exported by visone. Is there something missing in the DNA graphml file that is present in the visone graphml file that is mentioned in the error messages? Can Gephi open the graphml file from visone without any problems? These would be some first ideas on how to diagnose the problem.

I am currently busy writing a new DNA version and will not be able to look into this any time soon, but perhaps you can find the problem and report back.