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SpatialHackathon / SpaceHack2023

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Update proprocessing #216

Closed Jieran-S closed 9 months ago

Jieran-S commented 9 months ago

Since our transform data option is default log1p transformation. I added an additional scaling step for GraphST and SCAN-IT. Using parameters in their source codes.

GraphST: https://github.com/JinmiaoChenLab/GraphST/blob/main/GraphST/preprocess.py SCAN-IT: https://github.com/zcang/SCAN-IT/blob/main/examples/Slide-seq/scanit.ipynb

For reviewers:

  1. These are the only 2 methods I found using scaled data. Is there any other method I miss?

  2. BANKSY requires a lib-norm (not log-norm) preprocessing. What should we do about that?

shdam commented 9 months ago

I think it makes sense to update Banksy to preprocess as they recommend. I have changed the script accordingly.

shdam commented 9 months ago

Thinking about it, I also found a way to use the existing preprocessing workflow in bass - the script has been updated accordingly

niklasmueboe commented 9 months ago

For now we can leave it as implemented in this PR. In the future we might want to try out library size normalization as a preprocessing step in general anyway.