Hey, awesome plugin. I now have a reason to add links between my notes instead of copy/pasting the relevant parts, thanks for your work on this.
I think I saw you mentioning somewhere that the plugin API doesn't allow to display the graph in a popup window, and since your plugin need a lot of screen space, that would probably be the best solution. However, I noticed the Favorites plugin has an option to toggle visibility which could be a good option (please include a keyboard shortcut for it, though. It's missing from the Favorites plugin).
With this, it would be possible to have the graph in the main panel below the editor/preview, and collapse it when unneeded.