I just wrote a simple patch that you can apply on top of rtgraph3d-0.1 to draw in 3d egdes from graphviz dot language. Now, if you use my class, you can write code like this:
from gvglue import *

gvg = GvGlue()

bob_leponge = gvg.newItem("Bob l'eponge")
patrick = gvg.newItem("Patrick")
carlo = gvg.newItem("Carlo")
puff = gvg.newItem("Puff")
plankton = gvg.newItem("Plankton")

gvg.newLink(bob_leponge, patrick)
gvg.newLink(bob_leponge, carlo)
gvg.newLink(bob_leponge, puff)
gvg.newLink(bob_leponge, plankton)
gvg.newLink(patrick, carlo)

gvg.finish()

That will generate dot language, which is the graphviz language. Output the result in the file called "mydotfile.dot".

Then, run rtgraph3d using the following operations:
$ ./rtgraph3d.py &
$ ./rtg_cli.py
RTG> dot mydotfile.dot
RTG>



Of course, you don't need my class to generate graphviz dot language, I was just making some kind of advertisement ;-)

Thanks to Philippe for his involvement in the development of rtgraph3d, scapy, the security community in general and other very exciting projects.