I used to generate most of my diagrams in PlantUML[0], but recently found that my not-taking app, Joplin[1], has Mermaid built in.

PlantUML has the benefit that you can include it in your builds, e.g. parse any .plantuml files in `make doc` or in your CI.

But I like Mermaid more: its easier to read, less quirky and easily integratable in the markdown (or note-taking apps) without the need for extra build steps.

[0] https://plantuml.com/ [1] https://joplinapp.org/

One of my favorite applications in R that can make Graphviz like plots: http://rich-iannone.github.io/DiagrammeR/index.html