Is the data hierarchical? If it is, you could build a custom app that still uses Graphviz to build a graph where the hierarchical groups are initially collapsed, and then allow exploration of the graph by expanding nodes.

I just built something like this to visually explore the symbols in software code (variables, functions, classes, etc).

https://marketplace.visualstudio.com/items?itemName=AtomicConcepts.atomicviz