In saeyslab/FlowSOM_workshop: How to get started with FlowSOM

library(flowCore)
library(FlowSOM)
library(FlowSOMworkshop)
library(Rtsne)
library(ggplot2)

files <- list.files("../inst/extdata", 
                    pattern = "Live.fcs",
                    full.names = TRUE)

set.seed(1)
ff <- AggregateFlowFrames(files,
                          cTotal = 6*10000)
ff <- compensate(ff, ff@description$`$SPILLOVER`)
ff <- transform(ff, estimateLogicle(ff, colnames(ff)[7:19]))

fsom <- FlowSOM(ff,
                colsToUse = c(8:15, 17:19),
                scale = FALSE,
                nClus = 10,
                seed = 1)

PlotStars(fsom$FlowSOM)

set.seed(1)
subset <- sample(1:nrow(ff), 5000)

tSNE <- Rtsne(ff@exprs[subset, c(8:15, 17:19)])

to_plot <- data.frame(tsne_x = tSNE$Y[,1],
                      tsne_y = tSNE$Y[,2],
                      cluster = factor(GetClusters(fsom)[subset]),
                      metacluster = factor(GetMetaclusters(fsom)[subset]))

ggplot(to_plot) +
  geom_point(aes(x = tsne_x, y = tsne_y, col = metacluster))