local plotting

[Lioscro]

Support for plotting trees locally, instead of submitting to iTOL (since this is paid now...)

• Support rectangle plots in the four cardinal directions (left, right, up, down)
• Support polar plots (circular plots)
• Support colorstrip annotations (where categorical/continuous/indel information is displayed as a color strip)
• Support subclade coloring
• Static plotting using Matplotlib
• Interactive plotting using Plotly
• Tutorial notebook (https://nbviewer.org/github/YosefLab/Cassiopeia/blob/tree-plotter/notebooks/local_plotting.ipynb) -- Github doesn't render plotly plots when viewing notebook.

Samples (3730_NT_T1)

Polar

Rectangle

[codecov]

Codecov Report

Merging #159 (09f6c7c) into master (3e85462) will decrease coverage by 0.08%.
The diff coverage is 87.69%.

@@            Coverage Diff             @@
##           master     #159      +/-   ##
==========================================
- Coverage   87.11%   87.03%   -0.09%     
==========================================
  Files          73       75       +2     
  Lines        5130     5521     +391     
==========================================
+ Hits         4469     4805     +336     
- Misses        661      716      +55     

Impacted Files	Coverage Δ
cassiopeia/plotting/local.py	80.62% <80.62%> (ø)
cassiopeia/plotting/utilities.py	96.79% <96.79%> (ø)
cassiopeia/mixins/errors.py	100.00% <100.00%> (ø)
cassiopeia/mixins/warnings.py	100.00% <100.00%> (ø)
cassiopeia/plotting/__init__.py	100.00% <100.00%> (ø)
cassiopeia/plotting/itol_utilities.py	59.39% <100.00%> (-10.25%)	⬇️

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[mattjones315]

I'm really excited to take a look at this @Lioscro!

One quick comment -- I think this PR will really benefit from a little notebook tutorial. What do you think?

[Lioscro]

I'm really excited to take a look at this @Lioscro!

One quick comment -- I think this PR will really benefit from a little notebook tutorial. What do you think?

Of course! Keep in mind there are still a ton of things to add to this PR, so I'll get to that eventually.

[richardyz98]

Hi Joseph,
Amazing PR! The code is really clean and understandable. Thanks for this tremendous effort.

I had some clerical comments, but otherwise it looks really good.

Also, if I understand correctly, the plotting functions at the moment can only consume allele tables? I don't think it's in the scope of this PR, but perhaps we can add (and this is something I may be able to help on) functionality to consume character matrices as well?

Thanks!
Richard

[Lioscro]

Hi Joseph, Amazing PR! The code is really clean and understandable. Thanks for this tremendous effort.

I had some clerical comments, but otherwise it looks really good.

Also, if I understand correctly, the plotting functions at the moment can only consume allele tables? I don't think it's in the scope of this PR, but perhaps we can add (and this is something I may be able to help on) functionality to consume character matrices as well?

Thanks! Richard

I think that is a great idea! I'll open a new issue to implement this. I also considered doing that in this PR, but at the moment I just wanted to replicate all the important functionalities from iTOL plotting.

[mattjones315]

Wow! I am thoroughly impressed by this fantastic PR! I don't have anything I'd like to see changed per se, but before you merge this in, can you add these functions to the documentation website? I'm happy to help if you're unfamiliar with how our docs folder works. For this reason, I'll Request Changes until we get the docs updated.

[richardyz98]

Looks good to me Joseph! Thank you for clearing up all of my comments!

[mattjones315]

This looks fantastic! Thanks so much for the hard work here. The only thing missing is the notebook tutorial on the documentation site. I'll add that in here for you.