Application of PHATE to Visium 10x data

[tyaoi]

Hi,

For spatial trajectory inference in spatial transcriptome data, PHATE is more suitable than commonly used methods such as PCA and tSNE.

I think it would be more effective to integrate spatial distance using image data and incorporate it into spatial trajectory inference like stLearn, and after confirming that the tree structure assumption exists by PHATE, integrating spatial distance and inferring spatial trajectory may stabilize the estimation results.

tyaoi