R Notebook

# 
# i = "Comp Ctrl_Tube_002.fcs"
# file_full = paste0("C://Users/vht/Desktop/vhtran_data_dalia/DataFromChariff/DaliaData/DaliaAllfcs/",i)
# 
# 
# 
# C:\Users\vht\Desktop\vhtran_data_dalia\DataFromChariff\DaliaData\DaliaAllfcs
# 
# 
# 
# FCS = read.FCS(file_full)
# 
# 
# FCS1 <- (FCS@exprs)
# 
# hist(FCS1[,"FSC-A"], main = "Distribution of FCS-A /Comp_tube_002")
i = "Comp Ctrl_Tube_002.fcs"
file_full = paste0("C://Users/vht/Desktop/vhtran_data_dalia/DataFromChariff/DaliaData/DaliaAllfcs/",i)
FCS = read.FCS(file_full)
T2 <- as.data.frame(FCS@exprs)
colnames(T2)[which(colnames(T2)=="FSC-A")] <- "FSC-A"
colnames(T2)[which(colnames(T2)=="FITC-A")] <- "IgD"
colnames(T2)[which(colnames(T2)=="PE-A")] <- "CD24"
colnames(T2)[which(colnames(T2)=="PE-Texas Red-A")] <- "CD19"
colnames(T2)[which(colnames(T2)=="PE-Cy5-A")] <- "CD20"
colnames(T2)[which(colnames(T2)=="PE-Cy7-A")] <- "CD38"
colnames(T2)[which(colnames(T2)=="APC-A")] <- "CD138"
colnames(T2)[which(colnames(T2)=="APC-Cy7-A")] <- "CD27"
colnames(T2)[which(colnames(T2)=="Pacific Orange-A")] <- "CD45"
CD19_com = T2[,"CD19"]
FCS <- read.FCS("C://Users/vht/Desktop/vhtran_data_dalia/mydf/Bcell/ID01_03_000_ACC2432_Tube_002.fcs")
T2 <- as.data.frame(FCS@exprs)
head(T2)

colnames(T2)[which(colnames(T2)=="FSC-A")] <- "FSC-A"
colnames(T2)[which(colnames(T2)=="FITC-A")] <- "IgD"
colnames(T2)[which(colnames(T2)=="PE-A")] <- "CD24"
colnames(T2)[which(colnames(T2)=="PE-Texas Red-A")] <- "CD19"
colnames(T2)[which(colnames(T2)=="PE-Cy5-A")] <- "CD20"
colnames(T2)[which(colnames(T2)=="PE-Cy7-A")] <- "CD38"
colnames(T2)[which(colnames(T2)=="APC-A")] <- "CD138"
colnames(T2)[which(colnames(T2)=="APC-Cy7-A")] <- "CD27"
colnames(T2)[which(colnames(T2)=="Pacific Orange-A")] <- "CD45"
CD19 = T2[,"CD19"]
dd <- rbind(data.frame(value = CD19, id = 'CD19_Patient_01_00_Tube2'), data.frame(value = CD19_com, id = 'CD19_com_tube2'))
ggplot(dd, aes(x=value)) + 
  #geom_histogram(aes(y=..ndensity..)) + 
  geom_density(aes(colour = id)) + ylab("density") + xlim(0, 1000)

p1 = ggplot(dd, aes(x=value, fill=id)) + geom_histogram(alpha=0.4, position="identity") + xlim(-100, 1000)
p1 + xlab("Fluororescence intensity")