CountGroups {FlowSOM} | R Documentation |
Calculate differences in cell counts between groups
CountGroups(fsom, groups, plot = TRUE, silent = FALSE)
fsom |
FlowSOM object as generated by BuildSOM |
groups |
List containing an array with file names for each group |
plot |
Logical. If TRUE, make a starplot of each individual file |
silent |
Logical. If TRUE, print progress messages |
Distance matrix
set.seed(1) # Build the FlowSOM tree on the example file fileName <- system.file("extdata", "68983.fcs", package="FlowSOM") flowSOM.res <- FlowSOM(fileName, compensate=TRUE,transform=TRUE, scale=TRUE,colsToUse=c(9,12,14:18),nClus = 10) # Have a look at the resulting tree PlotStars(flowSOM.res[[1]],backgroundValues = as.factor(flowSOM.res[[2]])) # Select all cells except the branch that corresponds with automated # cluster 7 (CD3+ TCRyd +) and write te another file for the example # In practice you would not generate any new file but use your different # files from your different groups ff <- flowCore::read.FCS(fileName) ff_tmp <- ff[flowSOM.res[[1]]$map$mapping[,1] %in% which(flowSOM.res[[2]] != 7),] flowCore::write.FCS(ff_tmp,file="ff_tmp.fcs") # Make an extra file without cluster 7 and double amount of cluster 10 ff_tmp <- ff[c(which(flowSOM.res[[1]]$map$mapping[,1] %in% which(flowSOM.res[[2]] != 7)), which(flowSOM.res[[1]]$map$mapping[,1] %in% which(flowSOM.res[[2]] == 5))),] flowCore::write.FCS(ff_tmp,file="ff_tmp2.fcs") # Compare the original file with the two new files we made groupRes <- CountGroups(flowSOM.res[[1]], groups=list("AllCells"=c(fileName), "Without_ydTcells"=c("ff_tmp.fcs","ff_tmp2.fcs"))) PlotGroups(flowSOM.res[[1]], groupRes) # Compare only the file with the double amount of cluster 10 groupRes <- CountGroups(flowSOM.res[[1]], groups=list("AllCells"=c(fileName), "Without_ydTcells"=c("ff_tmp2.fcs"))) PlotGroups(flowSOM.res[[1]], groupRes)