Visualize whole tree of infections

[afmagee42]

Resolves #24 and #15. Solves #53 along the way because the broken plots that led to were driving me crazy.

Code lives in ringvax.plot, and I'm rather tempted to wrap it all up into a plotting object since that would avoid a lot of unneeded passing of objects around (the simulation, plotting parameters, and the plot itself).

Colors and styles can and probably should be argued over. I strove to keep things clean and visible first and foremost, but also to use our color palette and keep things accessible. I think this is mostly achieved, except perhaps marking detections which is a bit ugly. I tried delineating detection types by color, instead of shape, but I ran out of colors that were both easy to see on both latent and exposed backgrounds and which were truly distinctive from each other.

To keep some of the plotting-induced post-processing sane, I added infection attributes: the id and the infectees.

[swo]

Pretty cool!!

I'm guessing this is:

• Gray bars are latent
• Blue/teal/gray is infectious
• Green lozenge is passive detection(?)
• Orange lozenge is active detection(?)
• Gray ticks are onward infections that are not tracked

I could really use a legend or something!

Also, I would have expected to see:

• Index infection
• Contacts
• Contacts of contacts
• Contacts of contacts of contacts

But it looks like this is actually there is one more? This is telling me our default "number of simulated generations" should be 3, not 4? Does "simulated" include the index? I'll break this off as a separate issue (#62)

[swo]

This could definitely work. I have some questions to make sure we're going the right way first.

[swo]

I got an error about matplotlib, see #61

[afmagee42]

Re: legend and what things are: yes we need one, but I figured we should agree on the aesthetics we liked first.

E.g., I also have #64 (which is what I thought I had opened this PR on... oops... but you've got the right interpretation for what's been shown here)

which I think is in many ways better, but requires shapes for detection.

[afmagee42]

To-dos and to-considers from sync disc:

• Axis/axes
• Different color for un-simulated forward infections vs actual infections
• Generation labels for infections
• Do we want "empty" post-detection "counterfactual infectious"?
• Colors are... perhaps bland