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jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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Is it reasonable to select nearby spots for analysis to understand the effects of stroma spots on neighboring cells? #160

Open oghzzang opened 1 month ago

oghzzang commented 1 month ago

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?

sqjin commented 1 month ago

@oghzzang For the first question, it is better to include all spots and then look into the interactions between the two regions of interest.

For the second question, if you are interested in the differences of cell-cell communication across different phenotypes, you can follow the tutorial of comparison analysis. When combining all the data to create a single CellChat object, one will increase the power of the inference by utilizing the information from all slices.

bicorelab commented 1 month ago

Dear @sqjin Thank you for your detailed response. Many thanks.

Oh.