Codecov Report

Merging #881 (112cabb) into master (c66eff4) will decrease coverage by 2.34%. The diff coverage is 50.00%.

@@            Coverage Diff             @@
##           master     #881      +/-   ##
==========================================
- Coverage   76.11%   73.76%   -2.35%     
==========================================
  Files          26       26              
  Lines        2106     2150      +44     
==========================================
- Hits         1603     1586      -17     
- Misses        503      564      +61

Flag	Coverage Δ
unittests	`73.76% <50.00%> (-2.35%)`	:arrow_down:

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Impacted Files	Coverage Δ
lineage/BaumWelch.py	`72.89% <0.00%> (-6.70%)`	:arrow_down:
lineage/Lineage_collections.py	`0.00% <0.00%> (ø)`
lineage/plotTree.py	`0.00% <0.00%> (ø)`
lineage/states/StateDistributionGamma.py	`87.14% <0.00%> (-4.59%)`	:arrow_down:
lineage/tHMM.py	`96.15% <25.00%> (-1.89%)`	:arrow_down:
lineage/states/stateCommon.py	`94.44% <81.81%> (-1.02%)`	:arrow_down:
lineage/import_lineage.py	`96.37% <96.36%> (-1.13%)`	:arrow_down:
lineage/tests/test_import_lineage.py	`100.00% <100.00%> (ø)`

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Farnazmdi commented 2 years ago

This is almost done. I moved the 3 figures (BIC, analysis of HGF, and analysis of OSM) to the dropbox folder we have for resubmission in the figures folder, but they need a bit of attention from JC to look better. I will have to read about HGF and OSM effects on MCF10A to explain the results. I will do that tomorrow.

aarmey commented 2 years ago

Since the inter-treatment constraint is removed, you can just analyze all the treatments as one batch.

Farnazmdi commented 2 years ago

No sorry, not ready... When you say analyze all in one batch, do you mean just one BIC figure for all three conditions? Then we will let the states kind of separate the treatments?

aarmey commented 2 years ago

Aren't there four treatments? (PBS, EGF, HGF, OSM)

Yes, that's what I mean.

Farnazmdi commented 2 years ago

I am on it. I kept egf away, it was throwing an error.. but will try to resolve it.

Farnazmdi commented 2 years ago

It is ready for review. I ran the BIC a couple of times, all the time 6 states was optimal.