Sunday, July 3, 2016

Gephi and iGraph: graphml

When Gephi, which is great, decides to not exactly work, you can save your Gephi graph file in graphml format and then import it into R (or Python or C/C++) using iGraph so you can also draw it the way you were hoping to. (I'm having an issue with setting the colors at all in Gephi.)

It took me a few tries to figure out which format would work. I need location (since Gephi is good at that but I don't know how to make iGraph or R's SNA package do that) and attributes for the data. So far, so good!

Some helpful pages:

Note!!!! Apparently if you make a variable in R (at least while trying to graph something with plot) and you use a variable for your palette that you name palette, you will destroy (ok ok overwrite) some other official variable or setting also named palette, but the error you get will not at all clue you in to what happened. Better to call your variable my_palette or the_palette, which is what I usually do (so why didn't I do it here?).