Open FanZhang9 opened 2 years ago
I have fixed this problem by selecting the mutual cell type on 2 data set from the beginning. It taken me 1 day to figure it out.
I got a error when using netAnalysis_signalingChanges_scatter function. After checking my cellchat obj, I found cellchat@netP$centr is null. Actually, my cellchat is a merged cellchat list from chbm and chlm.
names(chlm@netP$centr[[1]])
[1] "outdeg_unweighted" "indeg_unweighted" "outdeg"
[4] "indeg" "hub" "authority"
[7] "eigen" "page_rank" "betweenness"
[10] "flowbet" "info"
names(chbm@netP$centr[[1]])
[1] "outdeg_unweighted" "indeg_unweighted" "outdeg"
[4] "indeg" "hub" "authority"
[7] "eigen" "page_rank" "betweenness"
[10] "flowbet" "info"
Here is my codes to merge cellchat obj. cellchat <- chbm cellchat <- aggregateNet(cellchat) cellchat <- netAnalysis_computeCentrality(cellchat, slot.name = "netP") chbm <- cellchat
cellchat <- chlm cellchat <- aggregateNet(cellchat) cellchat <- netAnalysis_computeCentrality(cellchat, slot.name = "netP") chlm <- cellchat
chbm <- updateCellChat(chbm) chlm <- updateCellChat(chlm)
object.list <- list(BM = chbm, LM = chlm) cellchat <- mergeCellChat(object.list, add.names = names(object.list)) After runnning the code, I got the info: Merge the following slots: 'data.signaling','images','net', 'netP','meta', 'idents', 'var.features' , 'DB', and 'LR'.
Hope your help. Any suggestions will be appreciated.
This is because your might have cell populations (clusters) that are not shared among both conditions. I had the same, and kept having the same error. If you take them out, the analysis runs smooth.
Thank you for your advice.
You can also lift up the cell identity to be the same (i.e., the union of the cell identities across two condtions)
On Wed, Jun 7, 2023 at 9:08 PM shanshenbing @.***> wrote:
Thank you for your advice.
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I believe that does not work, at least not will cellchat. I had the same identity active across all my samples, but if there's samples that contain 0 cells in one of the clusters from that identity, it won't run.
Hi, I have 4 cellchat object merged together, two objects have 4 cellgroups less than the other two objects. I used liftcellchat function to lift up the cell idents the same among all the 4 cellchat objects. But still I got the error when running netAnalysis_signalingChanges_scatter function. The error is : Error in outgoing[, i] <- centr[[i]][[x.measure]] : number of items to replace is not a multiple of replacement length
Any solution for the issue? Thank you Ting
I got the same problem, and I've tried all the solutions above. Still the error exists.
ERROR with the netAnalysis_signalingChanges_scatter
netAnalysis_signalingChanges_scatter(cellchat, idents.use = "Conventional_dendritic")
Merge the following slots: 'data.signaling','net', 'netP','meta', 'idents', 'var.features' , 'DB', and 'LR'. Visualizing differential outgoing and incoming signaling changes from CTL to SP Error in outgoing[, i] <- centr[[i]][[x.measure]] : number of items to replace is not a multiple of replacement length
This is my cellchat object I am trying to compare ; cellchat_mer.rdata.gz