Feature/threshold assignment#61
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irene-bonapa wants to merge 14 commits into
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This reverts commit 9558a26.
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Resolves #4
Re-implementation of ICON, adapted to our data format and scenario.
Short summary:
ICON calculates a S score and assigns specificity to all cells with
S > threshold, with:S = np.log(E+0.01) * R * C^2, followed by per cell normalisation and per dextramer scaling.E: Denoised dextramer signal.
dextramer_counts - background_noise, withbackground_noisean user input, or a high quantile of the negative control dextramer.C: pMHC ratio per cell.
E/sum(E, axis=1).R: clonal purity.
clonal_counts.div(clonal_counts.sum(axis=1), axis=0), with clonal counts the number of cells per clone with E>0 per dextramer.In the original ICON implementation, there's a bug in R calculation, that gives very low scores to clones with
R=1. For reproducibility, we implemented both options, withfaitfhul=Truerefering to the original ICON implementation.