I’ve also been playing with pinned nodes for the last few days trying to “solve” your other problem (Aspect ratio with neato or fdp - #5 by andrew). Lots of heartburn, probably one or more issues (to be written), no success.
I think both neato and fdp (haven’t checked other engines) don’t fully ignore pinned nodes, but do weird (unpredictable?) transforms.
Also, pinned nodes seem to define an overlay. The nodes are placed “on-top-of” the rest of the graph. Not what you want if you’re trying to create freespace/whitespace. Dang.
This needs more investigation, but I don’t expect a near-term solution that includes pinned nodes.
However, all is not lost (yet). I think there may other ways to solve (or improve) both problems.
I’m celebrating the 4th, so more complete response later, but can you say more about the whitespace:
- around nodes, edges, or “molecules”?
- if “molecules”, interior or exterior?
- which engines are you open to trying?
- can you hack up an example diagram to show the goal