Is it reasonable to select nearby spots for analysis to understand the effects of stroma spots on neighboring cells?

[oghzzang]

Dear @sqjin

Thank you for providing this valuable resource. I have two questions,

Q1. I want to understand the impact of stroma spots on neighboring cells. In such cases, is it reasonable to selectively analyze nearby spots along with stroma spots using cellchat? Alternatively, is it better to include all spots from spatial data and analyze them rather than selectively choosing nearby spots when conducting cellchat analysis?

Q2, I'm conducting research by performing Visium sequencing on 12 hepatocellular carcinoma tissues that exhibit completely different phenotypes. Would you recommend combining all the data in this case using this tutorial (Brief tutorial for CellChat analysis of multiple spatially resolved transcriptomic datasets)?Or is it recommended to check the results individually for each sample?