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
Groupstats
set.seed(1) 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) ff <- flowCore::read.FCS(fileName) # Make an additional file without cluster 7 and double amount of cluster 5 selection <- c(which(GetClusters(flowSOM.res) %in% which(flowSOM.res$metaclustering != 7)), which(GetClusters(flowSOM.res) %in% which(flowSOM.res$metaclustering == 5))) ff_tmp <- ff[selection,] flowCore::write.FCS(ff_tmp, file="ff_tmp.fcs") # Compare only the file with the double amount of cluster 10 features <- GetFeatures(flowSOM.res, c(fileName, "ff_tmp.fcs"), level = "clusters", type = "percentages") stats <- GroupStats(features$cluster_percentages, groups = list("AllCells" = c(fileName), "Without_ydTcells" = c("ff_tmp.fcs")))