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

### Value

Distance matrix

### Examples

       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)

[Package FlowSOM version 1.18.0 Index]