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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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problems in "Comparison analysis of multiple datasets with different cell type compositions" #8

Open GGboy-Zzz opened 10 months ago

GGboy-Zzz commented 10 months ago

Define the cell labels to lift up

group.new = levels(cellchat.E14@idents) cellchat.E13 <- liftCellChat(cellchat.E13, group.new)

> The CellChat object will be lifted up using the cell labels FIB-A, FIB-B, FIB-P, DC, Pericyte, MYL, Immune, ENDO, Muscle, MELA, Basal-P, Basal, Spinious

> Update slots object@net, object@netP, object@idents in a single dataset...

Hi, I have 4 development stage seura_object, which I ran cellchate and generated cellchatA/B/C/D. Their idents are not completely the same, should I define "group.new" according their union idents?

sqjin commented 10 months ago

@GGboy-Zzz Yes, you are correct and you should define "group.new" according their union idents.