all figures updated

[Farnazmdi]

This branch just updated all figures according to the new fitting. The only thing that I "changed" was that in the BIC figure, we were fitting and calculating for 1, 2, .., 7 states and pick the best number then run the model again with those number of states. What I did in this branch is that during the BIC fitting, I save the tHMMobjects and recall the one that we pick based on the BIC. This way the BIC value matches the tHMMobj we pick.

[codecov[bot]]

Codecov Report

Merging #952 (7995a40) into master (c3c75f8) will decrease coverage by 0.36%. The diff coverage is 9.09%.

@@            Coverage Diff             @@
##           master     #952      +/-   ##
==========================================
- Coverage   82.65%   82.29%   -0.37%     
==========================================
  Files          28       28              
  Lines        2243     2253      +10     
==========================================
  Hits         1854     1854              
- Misses        389      399      +10     

Flag	Coverage Δ
unittests	82.29% <9.09%> (-0.37%)	:arrow_down:

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Impacted Files	Coverage Δ
lineage/plotTree.py	0.00% <0.00%> (ø)
lineage/tests/test_BaumWelch.py	100.00% <100.00%> (ø)

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[aarmey]

@Farnazmdi this is failing because cell.state is None. Did you possibly pickle the tHMM objects before they were fit?

[Farnazmdi]

Sorry about this. I will fix it tonight. I saved all models created from BIC analysis (1, 2, 3, .. state tHMM objects) so we don't have to fit the model again with the optimal number of states. I have not assigned states to those tHMMobjs created from BIC fitting and pickled. This is failing probably in one or two figures that I forgot to add the state assignment code.

[aarmey]

That's reasonable. Just trying to help with where the problem lies.

I also think it's better to not commit these figure files. The pickle files now keep the results reproducible.

[Farnazmdi]

I removed all svg files that could be recreated. Had to make some changes to the functions to automatically generate those figures in the cartoon folder. This should be ready now. I will merge it if it is alright? The changes are mostly just to the figures, with a minor change to the BW test and the addition of a function to plotTree to create those samples of lineage trees we use in lapatinib and gemcitabine figures.

[aarmey]

Let me go through it carefully first. Will do so in a bit.

[Farnazmdi]

Thank you, merging..