Plotting gated FACS data

plot.R

library(ggplot2)
library(RColorBrewer)

d <- read.csv('BC4-R1-1.fcs_spill_applied_AID_BC_Cell_P1.txt', sep='\t', header=T, skip=1)
names(d) <- c('Event', 'FSC', 'SCC', 'FITC')

myPalette <- colorRampPalette(rev(brewer.pal(11, "Spectral")), space="Lab")

g <- ggplot(d, aes(y=FSC, x=FITC)) +
    geom_hex(bins=128) +
    scale_x_continuous(trans=logiclescale::logicle_trans()) +
    scale_fill_gradientn(colours=myPalette(10)) +
    theme_bw() +
    labs(x='GFP', y='FSC-A') +
    ylim(0, 200000)

ggsave(plot=g, filename='BC4-R1-1.pdf', h=5, w=5)