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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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10x visium spot proportion #126

Open wang0430 opened 7 months ago

wang0430 commented 7 months ago

Hi,

Thank you very much for developing such an excellent tool for cell communication, especially for the spatial transcriptome.

I am recently using cellchat to analyze the interaction of spatial transcriptome data. Similar to the 10x visium sequencing method, it cannot achieve single-cell resolution, so each point is actually the proportion of cells of multiple cell types. Cellchat must select the cell type with the highest proportion as a representative and then continue the analysis, which may greatly affect the reliability of the results. I sent you an email last year to raise this issue, and the reply said that the weight will be increased in the near future, but it seems that there is still no update. Sorry to trouble you!

best wishes,

wanggl

Mr-Byun commented 1 month ago

Hopefully, a CellChat implementation will soon be available to deal with capture spot proportions for 10X Visium #89. A study in 2023 seems to deal with this problem by performing c2c analysis across all spots, but the package appears to be limited for cancer data.