The most advanced calculator for Factorio is definitely YAFC, "Yet Another Factorio Calculator", based on Google's OrTools solvers [https://github.com/shpaass/yafc-ce]
(gifs readme at [https://github.com/shpaass/yafc-ce/blob/master/Docs/Gifs.md])
The flowcharts are generally made with Foreman2 [https://github.com/DanielKote/Foreman2], yet another external tool
Both the calculator websites, https://factoriolab.github.io and https://kirkmcdonald.github.io also have both Sankey and Box-line flow diagrams
In-game calculator mods are Rate Calculator (that just shows the production ratios of selection), Helmod and Factory planner, don't have flow diagrams afaik
---
But with the new 2.0 DLC Quality and Recycling mechanics which makes every graph connection quintuple and bidirectional, the difficulty to calculate what's the best way to craft something of high quality is going to skyrocket