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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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using cellchat on visium after single cell mapping with celltrek #442

Open kguion1 opened 2 years ago

kguion1 commented 2 years ago

Hi,

I am very excited to use your package! I am analyzing some visium data and hoping to leverage the spatial information provided after mapping single cells back to their spatial location. I noticed in the celltrek paper the following statement: "We conducted a cell-cell interaction analysis on the scRNASeq data using CellChat and used the scoloc graph to filter cell-cell pairs, assuming that colocalized cells have higher changes to interact with each other."

I am following your Full tutorial for CellChat analysis of a single dataset with detailed explanation of each function and am wondering at what point I should be "filtering cell-cell pairs" and if you had any code examples or insights into adding in this step for spatial consideration.

Any help would be appreciated!

Thank you!

sqjin commented 2 years ago

@kguion1 This filter step can be added after running computeCommunProb. Basically, you can filter out the interactions that are spatially distant from each other. We are still working on the new version of CellChat for spatial transcriptomics, but at this moment, you can try other colocalization method and simply focus on the cell pairs that were neighbors.