it's pretty basic topology - embedding versus immersion. you cannot embed anything but the simplest software in a 2d plane. you end up having to endlessly try to structure things to minimize line crossings, make multiple diagrams of the same code to capture different aspects of it, or otherwise perform perversions just so it fits on a page.

And I live through this. most of my early career was DoD related in the early '90s, when things like functional analysis was all the rage. endless pages of circles and lines which were more confusing than helpful, and certainly didn't actually capture what the software had to do. Bever again.