Add Tree.draw_tikz() to output tex/tikz drawing code.

[grahamgower]

[grahamgower]

Ping @gtsambos.

[gtsambos]

fyi @grahamgower, I'm forking this now so I can play around with getting mutations in here

[gtsambos]

Hi @grahamgower, I've created a PR against your fork (let me know if you have trouble with this). The additional code puts mutations on the plots, like this:

So far the code assumes mutation times aren't known -- but the case when they are shouldn't be difficult either, will look into it later this weekend

[grahamgower]

Thanks, that looks great!

[grahamgower]

and, TreeSequences...

[codecov[bot]]

Codecov Report

Merging #798 (faaac9c) into main (a7413ff) will decrease coverage by 6.37%. The diff coverage is 8.87%.

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@@            Coverage Diff             @@
##             main     #798      +/-   ##
==========================================
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==========================================
  Files          27       24       -3     
  Lines       23035    19558    -3477     
  Branches     1079     3686    +2607     
==========================================
- Hits        21561    17060    -4501     
+ Misses       1440     1403      -37     
- Partials       34     1095    +1061     

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c-tests	?
c_tests	85.33% <ø> (?)
lwt-tests	?
python-c-tests	?
python-tests	?
python_c_tests	89.13% <8.87%> (?)
python_tests	96.44% <8.87%> (?)

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Impacted Files	Coverage Δ
python/tskit/drawing.py	86.91% <8.73%> (-12.51%)	:arrow_down:
python/tskit/trees.py	96.93% <9.52%> (-1.02%)	:arrow_down:
c/tskit/stats.c	69.14% <0.00%> (-16.02%)	:arrow_down:
python/_tskitmodule.c	82.99% <0.00%> (-8.86%)	:arrow_down:
c/tskit/tables.c	81.27% <0.00%> (-8.63%)	:arrow_down:
c/tskit/haplotype_matching.c	90.42% <0.00%> (-4.64%)	:arrow_down:
c/tskit/convert.c	87.50% <0.00%> (-4.55%)	:arrow_down:
c/tskit/trees.c	90.45% <0.00%> (-4.41%)	:arrow_down:
c/tskit/genotypes.c	90.50% <0.00%> (-3.40%)	:arrow_down:
c/tskit/core.c	94.08% <0.00%> (-3.01%)	:arrow_down:
... and 14 more

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[gtsambos]

very nice 👀 I'd like to get a handle on the TreeSequence-wide draw_tikz method too, perhaps I could do some minor fixups on that to help me learn my way around it? I'm thinking scaling all the trees according to the max root time, and perhaps also adding axis labels

[grahamgower]

Yeah, adding the scaling and axes would be really useful. Just give me a moment, I've changed to use a \pic, and need to commit that.

[grahamgower]

Ok, have at it @gtsambos! Now we can do silly things like this:

import msprime
ts = msprime.simulate(10, recombination_rate=1, mutation_rate=1, random_seed=1)
ts.draw_tikz(
    "/tmp/s.tex",
    tree_height_scale="rank",
    standalone=True,
    preamble="\\usetikzlibrary{3d, shapes.geometric}",
    style="""%
        every pic/.append style={canvas is zy plane at x},
        mutationlabels/.append style = {
            opacity=0,
        },
        mutations/.append style = {
            star,
            star point ratio=2.5,
        },\
        """
)

[grahamgower]

With bigger sample sizes (n=1000, with 19 trees) I get: ! TeX capacity exceeded, sorry [main memory size=5000000]. Maybe we can structure things differently to improve this, but it's likely we're not going to be able to scale as well as for svg.

[grahamgower]

The solution for large drawings is to compile with lualatex, rather than pdflatex. It took a minute or two, but was actually quicker than calling draw_svg(). I guess this is beyond the limit of what's sensible.

msprime.simulate(1000, recombination_rate=1, mutation_rate=1, random_seed=1)

$ ls -lh /tmp/s.{tex,pdf,svg}
-rw-r--r-- 1 grg grg 4,5M Aug 29 10:15 /tmp/s.pdf
-rw-r--r-- 1 grg grg  16M Aug 29 10:23 /tmp/s.svg
-rw-r--r-- 1 grg grg 1,5M Aug 29 10:14 /tmp/s.tex

[gtsambos]

With bigger sample sizes (n=1000, with 19 trees) I get: ! TeX capacity exceeded, sorry [main memory size=5000000]. Maybe we can structure things differently to improve this, but it's likely we're not going to be able to scale as well as for svg.

The solution for large drawings is to compile with lualatex, rather than pdflatex. It took a minute or two, but was actually quicker than calling draw_svg(). I guess this is beyond the limit of what's sensible.

I wouldn't be too worried about this -- I doubt people will be using draw_tikz on this kind of scale.

[jeromekelleher]

Yeah, I'm 100% not worried about rendering large trees within tex. This is fundamentally for printed page output, so if it's too big to go on a printed page we don't care about it.

[benjeffery]

@grahamgower does this need tests to be mergable? Or are there still open questions about the implementation?

[grahamgower]

Probably tests and docs are the biggest things outstanding. And making sure the API is consistent enough with the other drawing functions would be a good idea.

[grahamgower]

Rebased. I'll take another look though this in the coming week.

[jeromekelleher]

This is really useful and a great addition, but I'm gone off the idea of incorporating it into tskit. Our experience with the SVG viz is that it quickly turns into a lot of code, and it's quite hard to test. In this case, we'd need to pull in a tex engine to CI and for all of our client side dependencies. Keeping consistency between the various viz APIs is a pain also.

@benjeffery, I'm guessing you're in a similar mind?

So, I suggest spinning it out into an independent project? tstikz or something?

[benjeffery]

So, I suggest spinning it out into an independent project? tstikz or something?

I think this is probably the right thing to do, and that maybe even the svg code is hefty enough not be in tskit, but that is another discussion!

[hyanwong]

Does this belong in https://github.com/tskit-dev/tsviz ? Perhaps we could move the PR over there and eventually merge it?

[benjeffery]

Does this belong in https://github.com/tskit-dev/tsviz ? Perhaps we could move the PR over there and eventually merge it?

Sounds good to me!