Amusingly, graphviz had dotty way back in the day so that you could adjust by hand. Now, it looks like they have gvedit. I haven't tried that one. That said,

Amusingly, graphviz had dotty way back in the day so that you could adjust by hand. Now, it looks like they have gvedit. I haven't tried that one. That said, the ability to "fix" the location of some items by providing it in the dot file is a feature most folks seem to ignore. Or not know exists.