Add ability to plot annotations (e.g. genes) along the x-axis

[hyanwong]

Description

Fixes #3000

PR Checklist:

• Tests that fully cover new/changed functionality.
• Documentation including tutorial content if appropriate.
• Changelogs, if there are API changes.

[hyanwong]

Example:

import msprime
ts = msprime.simulate(2, length=10, mutation_rate=1, random_seed=9)
ts.draw_svg(x_axis=True, size=(400, 300), x_regions={(1, 3): "foo", (3.2, 5): "bar"})

Also works if trees are skipped:

import msprime
ts = msprime.simulate(2, length=10, mutation_rate=1, recombination_rate=0.2, random_seed=9)
ts.draw_svg(x_axis=True, size=(800, 300), max_num_trees=4, x_regions={(0.5, 3): "foo", (5, 6): "bar"})

I think it should be up to the user to hide X tickmarks if they are deemed to get in the way of the annotation labels, as in the example above. E.g. that could be done by style=".x-axis .tick:nth-child(3) text {display: none}"

[codecov]

Codecov Report

Attention: Patch coverage is 95.83333% with 2 lines in your changes missing coverage. Please review.

Project coverage is 89.80%. Comparing base (56a163e) to head (979da99).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
python/tskit/drawing.py	95.83%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3002   +/-   ##
=======================================
  Coverage   89.79%   89.80%           
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  Files          29       29           
  Lines       31917    31931   +14     
  Branches     6175     6179    +4     
=======================================
+ Hits        28660    28675   +15     
  Misses       1860     1860           
+ Partials     1397     1396    -1     

Flag	Coverage Δ
c-tests	86.68% <ø> (ø)
lwt-tests	80.78% <ø> (ø)
python-c-tests	89.03% <ø> (ø)
python-tests	99.01% <95.83%> (+0.01%)	⬆️

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Files with missing lines	Coverage Δ
python/tskit/trees.py	98.80% <ø> (ø)
python/tskit/drawing.py	99.32% <95.83%> (+0.09%)	⬆️

[hyanwong]

I picked yellow region boxes for no particular reason, other than we are unlikely to use that colour for anything else (yellow symbols are generally impossible to see). I should probably add a tutorial example if this addition is thought to be useful.

[jeromekelleher]

Nice, I like it.

What happens when you have overlapping regions (which will happen, I'd imagine)?

[hyanwong]

Nice, I like it.

What happens when you have overlapping regions (which will happen, I'd imagine)?

We just plot overlapping boxes. I guess that's fine? If people want to distinguish them they can colour them using transparency. Actually, I think it would be good to make the boxes semi-opaque by default, so people notice if there are overlaps. A 50% opacity example is below: this LGTM, so I'll change the default style to that, unless anyone objects.

[jeromekelleher]

LGTM!

[petrelharp]

This is excellent!