Dimension of 'distance' in LR permutation test

BiomedicalMachineLearning / stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data

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Dimension of 'distance' in LR permutation test #255

Closed joan-yanqiong closed 3 months ago

joan-yanqiong commented 8 months ago

Hi,

I started started exploring xenium data and was trying out the tutorial. For the st.tl.cci.run function, one of the inputs is 'distance'. I was wondering what the dimension of that is. I saw that None means, immediate neighbours and 0 for within-spot. I don't have immediate neighbours, so I have to increase the distance. Is the distance just the number of spots in the grid?

duypham2108 commented 8 months ago

The distance is the pixel length as the radius from each spot center. We will query all the spots within that radius