I found this thread because I was looking for a way to bunch together/group nodes in the graph by their proximity in the folder hierarchy. Notes that only share the same root folder would push each other further away, whilst those in the same sub-sub-sub-folder would pull together. With these two rules it should already cause the grouping to happen quite naturally, and if they were sliders in the already existing graph, one can tweak them to their liking (even disabling them fully).