CountGroups {FlowSOM}R Documentation

Calculate differences in cell counts between groups

Description

Calculate differences in cell counts between groups

Usage

CountGroups(fsom, groups, plot = TRUE, silent = FALSE, ...)

Arguments

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

...

Extra arguments to be passed on to the PlotStars function

Value

Distance matrix

See Also

PlotStars,PlotGroups

Examples

   library(FlowSOM)
   set.seed(1)
   
   # Build the FlowSOM tree on the example file
   fileName <- system.file("extdata","lymphocytes.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)


[Package FlowSOM version 1.14.1 Index]