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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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missing pathways #656

Open Imm123 opened 1 year ago

Imm123 commented 1 year ago

Hi, After merging 3 cellchat objects, I am trying to create a bubble plot: netVisual_bubble(cellchat, sources.use = c("cell1", "cell2"), targets.use = "cell3", comparison = c(1,2,3), angle.x = 45, remove.isolate = T) I got all significant L-R interactions (including IL16 and IL17)

however when I select a signaling pathways: netVisual_bubble(cellchat, sources.use = c("cell1", "cell2"), targets.use = "cell3", comparison = c(1,2,3), angle.x = 45, remove.isolate = T, signaling = c("IL16")) I got this message: Cannot find IL16 . Please input a correct name!

What could be the problem in this case?

Best,

sqjin commented 1 year ago

@Imm123 This is an expected. You can either run the source codes or share your cellchat object with me to do it.

Imm123 commented 1 year ago

Thanks! How can I share the data with you privately? email?

orange-3711 commented 9 months ago

@Imm123 I met the same problem, can you tell me your problem solved?

sqjin commented 9 months ago

@orange-3711 This is probably due to the fact that the IL16 signaling does not appear when you specify sources.use = c("cell1", "cell2"), targets.use = "cell3"

orange-3711 commented 9 months ago

@sqjin Thanks for your answer, I see where the problem lies. This problem also arises when this signal is not present in one of the groups when multiple group comparisons are made. At present, my solution is to export the subset data with this signal in the comparison. Is there a better solution?