Visualizing the edges at scale doesnt yield nice results in general. It's simply too noisy.

The way to do it is to reduce the graph to some 300d or 500d embeddings, then use TSNE/UMAP/PACMAP to reduce that to 3d. Then visualize.

My prefered way is to use some first order embedding method like GGVec in this library [1] (disclaimer I wrote it). Node2Vec and ProNE don't yield great embeddings for visualization (the first is too filamented, the second too close to the unit ball).

Another great library to do this work is GRAPE [2]. Try first-order embedding methods, or short walks on second order methods to avoid the embeddings being too filamented by long random walk sampling.

[1] https://github.com/VHRanger/nodevectors

[2] https://github.com/AnacletoLAB/grape/