I have an R workflow that loads a folder of 24 .fcs files that have already been cleaned up and downsampled to 10,000 events into a formal class flowSet. The R script then transforms the @exprs matrix, runs flowSOM and UMAP on these data. These algorithms produce data frames that as 240,000 rows long (24 files x 10,000 events).

How do I get these three extra columns added to the 24 flowFrames within the flowSet?

Some of my code is below:

#Add data
path = "~/Desktop/Test"
files <- list.files(
  path = path, pattern = "\\.fcs$", full.names = TRUE
)

d_flowSet <- read.flowSet(
  files, transformation = FALSE, truncate_max_range = FALSE
)
setwd("~/Desktop/Test")

cols_lineage <- c(7,9:34)

#################
### Run UMAP ###
################

umap.out<-umap(somedata[cols_lineage])
head(umap.out)
plot.umap<-as.data.frame(umap.out$layout)
# Basic scatter plot of mpg according to cyl
plot(plot.umap,type="p",main="UMAP data", xlab='UMAP_X',ylab='UMAP_Y')

#################
### Export Data ###
################

cluster<-rowData(out_DA$d_se)
cluster<-cluster[,4]
UMAP_X<-umap.out$layout[,1]
UMAP_Y<-umap.out$layout[,2]

app.data<-as.matrix(cbind(cluster,UMAP_X,UMAP_Y))

How do I add this final app.data to the original slowSet?

If you don't mind a little detour, you can use fr_append_cols from the flowCore package to append those columns.

new_frame <- fr_append_cols(d_flowset[[1]], app.data)

Note that you need to provide the flowFrame (i.e. single FCS file) instead of the flowSet. You can then iterate with for-loop or apply functions to do it for all flowFrame that you have. Don't forget to name the columns of your app.data!