Remove plot_subgraph

[jeromekelleher]

I think we should remove the plot_subgraph method from this repo as it's generally been replaced with the ARG-visualiser and it'll be work to test and maintain. We can either move it to the paper repo (if we're going to use it there) or just delete, I don't really mind.

@hyanwong, what's your preference here?

[hyanwong]

We should definitely remove it from this repo. There are two reasons we might want to keep it in the paper repo:

1. For the paper, we might want a way to make plots that aren't just screenshots of the tskit_arg_visualizer output. I could imagine removing the graph-node placement code from the current plot_subgraph method, and getting that from the ARG visualizer though
2. currently the tskit_arg_visualizer doesn't quite do what we want, which is to be able to selectively expand nodes on the route up or down from the focal node of interest. However, the best route here would be to expand the capabilities of the tskit_arg_visualizer instead, I think (I will open an issue)

For the moment, I think we can move the method wholesale into the paper repo, then tweak to fit the tskit_arg_visualizer output.

[jeromekelleher]

SGTM. Would you like to copy it over into the right place? I can take care of deleting things here