there is no package called ‘CellChat’ about cellchat HOT 8 CLOSED

@zh-Bian Can you show me several lines of codes before you run this function and how you run this function?

from cellchat.

I followed the process of 'Walkthrough - CellChat analysis of cell-cell communication in mouse skin wounds'. Here are my codes.

cellchat <- subsetData(cellchat) # subset the expression data of signaling genes for saving computation cost
future::plan("multiprocess", workers = 15) # do parallel
cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)
cellchat <- projectData(cellchat, PPI.mouse) #human/mouse

library(CellChat)

cellchat <- computeCommunProb(cellchat)
cellchat <- computeCommunProbPathway(cellchat)
cellchat <- aggregateNet(cellchat)

When it run to 'cellchat <- computeCommunProb(cellchat) ', it failed with " 'there is no package called ‘CellChat’ ". Then I used the source code to test and I found the error occured in function computeExpr_complex(). @sqjin

data.complex = my.sapply(
X = 1:nrow(Rsubunits),
FUN = function(x) {
RsubunitsV <- unlist(Rsubunits[x,], use.names = F)
RsubunitsV <- RsubunitsV[RsubunitsV != ""]
return(geometricMean(data.use[RsubunitsV,]))
}
)

from cellchat.

@zh-Bian I have no idea on this error for now. I searched the similar issue online, and you might can try library.path <- .libPaths() library("cellchat", lib.loc = library.path). Please check here. If it does not work, can you share your cellchat object with me or your colleague?

from cellchat.

@zh-Bian library.path <- .libPaths(); library("CellChat", lib.loc = library.path)

from cellchat.

Hello, Thank you for your advice. I tried your method but it didn't work. And I noticed an interesting detail: when I first open my Rstudio, 'cellchat <- computeCommunProb(cellchat)' works fine, however the second is the same wrong. I think whether the function needs to access some resources online, so it sometimes works and sometimes not. @sqjin

from cellchat.

@zh-Bian I will take a look and fix this issue. For now, please just run this function only one time.

from cellchat.

OK. The way for me to use the package is interesting, and the package is useful. Thank you very much for answering my questions.

from cellchat.

@zh-Bian Hello, just let you know that I have no issue to rerun cellchat <- computeCommunProb(cellchat) in the same Rstudio.

from cellchat.