CountGroups: Calculate differences in cell counts between groups

In saeyslab/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

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

See Also

GroupStats

Examples

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")))

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.