Add permutation method to calculate thresholds #74
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Add permutation method to calculate thresholds
In this PR, we use a permutation method to randomly shuffle the whole rows (single-cells) and compute EMD per feature to get a single median value to represent the threshold where there is no change. Since EMD is not signed, we will add sign to this value in the figures to create a range.
We could not do the traditional shuffling independently per feature because it drastically changed the distributions per population, leading to large EMD values. When we shuffled whole rows, we can keep the same distribution which is what EMD is most sensitive to. I can explain this more in person if this doesn't make sense currently.