FACS data plotting

FACS data plotting (geom_hex)

# this code is about
# reading fcs files (from FACS) and converting them to one dataframe
# plotting is then done normally in ggplot
# installation instructions for the required libraries can be found on the internet:)

library(flowCore)
library(tidyverse)

 
### this function reads a fcs file and returns the data as a tibble, adding a column with the file name #####

read.fcs <- function(x) {
df <- read.FCS(x) %>% exprs() %>% as.tibble() %>% mutate(sample = x)
return(df)
}
################################################################################################################

# then read all files in one df, using map
# you have to be in the directory with your fcs files, e.g. use setwd("/path-to-directory")

files <- list.files(pattern = "*.fcs")
df <- map_df(files, read.fcs)

# optional, in the following line I just order the samples the way I want them in the plot
# df <- df %>% mutate(sample = factor(sample, levels = c("A06 E16 no NR.fcs", "A08 op no NR.fcs", "A07 E16 with NR.fcs", "A09 ope with NR.fcs")))

# after that you have to play with the plotting to get what you want

df %>% 
  ggplot() + 
  geom_hex(aes(`FSC-A`, `FL3-A`), bins = 128, alpha = 1) + 
  theme_bw() + 
  facet_grid(~ sample) + 
  scale_y_continuous(limits = c(0, 250000)) +
  scale_x_continuous(limits = c(0, 1e6)) +
  scale_fill_distiller(palette = "Spectral", trans = "sqrt") +
  geom_abline(slope = 0.12, alpha = 0.3, color = "black")