[differential abundance][dataset?] Adding condition label simulation with IDW

openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics

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[differential abundance][dataset?] Adding condition label simulation with IDW #256

Open emdann opened 3 years ago

emdann commented 3 years ago

Updating implementation of differential_abundance.datasets.utils._simulate_treatment to generate condition labels with IWD approach. Should include:

Picking minima/maxima with geosketching on PHATE or diffusion map dimensions. Indices get stored in the anndata.uns
Fast interpolation approach
incorporate parameters to control (A) size of DA region (B) DA effect size

@dburkhardt could you push to your preferred DA branch the working implementation you have?

emdann commented 3 years ago

A good addition to this would be to add some noise to single replicates, to model variability between samples. @dburkhardt wdyt?