I actually just started doing this in my architecture notes.

You can inline source code in org-mode that renders a graph png.

  #+BEGIN_SRC dot
  digraph {
    a -> b
    b -> a
  }
  #+END_SRC

You can look into graphviz and dot language for intricacies. Once you learn it, it's super useful to jot down ideas and change structures on the fly.

Very cool, thanks for sharing.