Network visualization

Which tools to use?

There are many many tools and the choice depends on the objective.

For a static visualization, the go-to tools are Gephi and Cytoscape. With either of these, publication-quality visualizations can be easily created. There are multiple formats, but I recommend creating two data files: node properties and edge properties. The node property file is indexed by the node id and contains node label, size, category, and various variables that can be used to style nodes. The edge property file would be indexed by the source and target node id pairs and contains various properties about the edges (weight, category, etc.). Both Gephi and Cytoscape can read these files and it is easy to convert to other formats as well.

If it requires interactivity and/or should be on the web, there are quite a few javascript-based visualizations. Vega and D3.js support several basic network visualizations: https://vega.github.io/vega/examples/ and https://observablehq.com/@d3/gallery. (D3.js provides more flexibility) There are also specialized tools such as http://sigmajs.org/ (works with the Gephi formats), https://js.cytoscape.org/, https://github.com/dblarremore/webweb, etc. Any general visualization libraries (D3.js, p5.js, etc.) can also be used for more customized visualizations.