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earmingol / cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
BSD 3-Clause "New" or "Revised" License
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extract LR pairs in each factor #22

Closed Wulin-Tan closed 1 year ago

Wulin-Tan commented 1 year ago

Hi, cell2cell team cell2cell and tensor-cell2cell are amazing tools and can perfectly fit my project. with the tutorial, I can construct the tensor and run the tensor-cell2cell pipeline. But how can I extract all LR pairs in each specific factor?

Wulin

earmingol commented 1 year ago

Hi @Wulin-Tan

I recommend taking a look at this notebook, particularly to the last part: https://earmingol.github.io/cell2cell/tutorials/ASD/02-Factor-Specific-ASD/

If you want to prioritize top LR pairs per factor, you can change this parameter loading_threshold. If you want to include all LR pairs, just assign loading_threshold=0.

Also, you may try using use_zscore=False for using the raw loadings from the decomposition and compare them across factors.

I hope this helps.

Erick