#Load the packages

library(flowCore)

library(flowAI)

library(ggcyto)

#How to get help

??flowCore

#Load a single file

myfile <- "C:/Users/chall/Downloads/FlowRepository_FR-FCM-ZZZU_files/0004.FCS"

fcsfile <- read.FCS(myfile)

fcsfile

names(fcsfile)

exprs(fcsfile)

each_col(fcsfile, median)

keyword(fcsfile)

#Compensation

spillover(fcsfile)

fcsfile_comp <-compensate(fcsfile, spillover(fcsfile)$SPILL)

fcsfile_comp

#Cleaning

fcsfile_comp_clean <- flow_auto_qc(fcsfile_comp)

fcsfile_comp_clean

keyword(fcsfile_comp_clean) <- keyword(fcsfile)

fcsfile_comp_clean

??flowAI

#Transformation

trans <- estimateLogicle(fcsfile_comp_clean, colnames(fcsfile_comp_clean[,3:10]))

fcsfile_comp_clean_trans <- transform(fcsfile_comp_clean, trans)

#Visualise the results

??ggcyto

autoplot(fcsfile_comp_clean)

autoplot(fcsfile_comp_clean_trans)

autoplot(fcsfile_comp_clean_trans, x="PE-Cy7-A", y="PerCP-Cy5-5-A", bins = 256)

autoplot(fcsfile_comp_clean_trans, x="Time", y="FSC-A", bins = 128)

autoplot(transform(fcsfile_comp,trans), x="Time", y="FSC-A", bins = 128)

#In a flowSet

myfiles <- list.files(path="C:/Users/chall/Downloads/FlowRepository_FR-FCM-ZZZU_files", pattern=".FCS$")

fs <- flowCore::read.flowSet(myfiles, path="C:/Users/chall/Downloads/FlowRepository_FR-FCM-ZZZU_files/")

fs

fs[[1]]

spillover(fs[[1]])

fs_comp <-compensate(fs, spillover(fs[[1]])$SPILL)

fs_comp_clean <- flow_auto_qc(fs_comp)

trans <- estimateLogicle(fs_comp_clean[[1]], colnames(fs_comp_clean[[1]][,3:10]))

fs_comp_clean_trans <- transform(fs_comp_clean, trans)

#fsApply

??fsApply

fsApply(fs,each_col,median)