So the linkages for the visualizations are derived from the notes themselves?

Yeah, that entire article is generated from the set of notes. There's one note for each subsection (down to the finest level of granularity) and it just extracts the article directly based on the links. I described this in a set of notes that end up here: https://github.com/alefore/weblog/blob/master/zettelkasten.m...

The images (e.g., distribution of back links per file, semilattice view, etc.) are also just generated programmatically from the repository of notes.

The code that extract it is here: https://github.com/alefore/edge/blob/master/rc/editor_comman... (function zke, which receives the output path, the path to the initial note, and a string listing space separated paths of notes to ignore).

Here's another example of an article generated from my notes (this is way longer and is very incomplete, and probably contains a bunch of mistakes, but you may find it interesting as an example): https://github.com/alefore/weblog/blob/master/software-corre...