Visualisation of graphs is a separate research area. There are a lot of software (applications, libraries) in this area. It would be hard to cover everything, but some examples are:
Standalone applications:
- graphviz (also available as JS/WASM library)
- gephi
- graphia
- Visualising algorithms at isohale
- tulip
- tmap
JS libraries:
- Cytoscape.js (also available as desktop applications)
- awesome-web-visualization-frameworks
JS libraries using WebGL:
See also: WebGL-WebGPU-frameworks-libraries
Python
Science papers: