SIGNALING NOT APPEARING

[zara03]

HI i am running cellchat on my data but i am unable to find il17 signaling in any of dataset i analyzed.Is it possible that its missing or its not in database? Kindly rep

[sqjin]

@zara03 Please check the suggestions in the tutotial.

If very well-known signaling pathways in the studied biological process are not predicted, USER can try truncatedMean with different trim values. The function computeAveExpr can help to check the average expression of signaling genes of interest, e.g, computeAveExpr(cellchat, features = c("CXCL12","CXCR4"), type = "truncatedMean", trim = 0.1).

[zara03]

Hi I tried the code and it worked but in feature plot of data i have IL17RC in Cholangiocytes while IL17RA in neutrophils while IL17A is expressed by DNT, but when i am trying to generate Chord diagram it gives other results. When i make enriched Violnplots in cellchat it gives what i see in feaature plots of data. What could be possible reasons? Code i used is ;

library(CellChat)

# cellchat <- createCellChat(cell, assay = "SCT") # CellChatDB <- CellChatDB.mouse dplyr:: glimpse(CellChatDB$interaction) # CellChatDB.use <- CellChatDB cellchat@DB <- CellChatDB.use # cellchat <- subsetData(cellchat) cellchat <- identifyOverExpressedGenes(cellchat) cellchat <- identifyOverExpressedInteractions(cellchat) cellchat <- computeCommunProb(cellchat,type = "truncatedMean", trim = 0.025) cellchat <- filterCommunication(cellchat, min.cells = 10) cellchat <- computeCommunProbPathway(cellchat) cellchat <- aggregateNet(cellchat) # # cellchat@netP$pathways # pathways.show <- c("IL17") #

Chord diagram

par(mfrow=c(1,1)) netVisual_aggregate(cellchat, signaling = pathways.show, layout = "chord") # netAnalysis_contribution(cellchat, signaling = pathways.show) plotGeneExpression(cellchat, signaling = "IL17",enriched.only = TRUE) # IL17-LR-3M.pdf [IL17A-1.pdf](https://github.com/sqjin/CellChat/files/11336919/IL17A-1.pd IL17RA-1.pdf IL17RC-1.pdf

f)

I have attached code and all plots IL17R-LR-ENRICHRD.pdf

IL17-3M.pdf