How does stlearn calculates the number of L-R pairs of celltype

BiomedicalMachineLearning / stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data

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How does stlearn calculates the number of L-R pairs of celltype #288

Open caiquanyou opened 8 months ago

caiquanyou commented 8 months ago

How does stlearn calculates the number of L-R pairs of celltype? which part I should usor any code for tutorial. For example, I run st.tl.cci.run_cci, and how could I get total interactive LR pair of cell A and cell B

duypham2108 commented 8 months ago

You can check the description of the function here. I am not sure I got your question right, but you can set the sig_spots=0 and lower other parameters like min_spots https://github.com/BiomedicalMachineLearning/stLearn/blob/bf917588de6503d0f8f93b59951a2dd9232e4a7a/stlearn/tools/microenv/cci/analysis.py#L510-L591