Reproducing Supplementary Figure 13 in paper and general re-weighting procedure

[jashahir]

Hi, first off, great algorithm! I've used PHATE in my own work with very encouraging results and appreciate its clarity in studying continuous biological processes versus the more conventional tools (e.g., tSNE, UMAP). I'm curious as to how to reproduce the supplementary figure 13 from your paper where you re-weight distances to highlight different biological processes (i.e., differentiation, cell cycle, mitosis) in the same data. Specifically, (1) how does this re-weighting process work (both in theory and implementation in PHATE), (2) how do you choose which genes to up-weight for each process, and (3) does this introduce any biases in downstream analyses (e.g., differential expression, RNA velocity)? I couldn't find any code to reproduce them or how to do this re-weighting in general in PHATE, nor a detailed description of the math behind it in neither the main paper nor supplement.

Thanks!!