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The development version of this package supports graph animation (not yet on CRAN): https://github.com/bwlewis/rthreejs

If you're in R this might work: https://github.com/statnet/ndtv

Depending on the number of time points you can use the facetting functions in ggraph to create small multiples

About 10,000 relations, each with a unique point in time. Looks like the facet isn't quite what I want.

You can of course animate it like this https://twitter.com/thomasp85/status/694905779539812352 but a static representation is often easier to interogate. I would try to bin the time points and facet on them...

Sacha Epskamp's tutorial has a nice section on this:

Also the section on penalized Ising models is great, I haven't seen anything else like it.