FACS plot with user-defined gate

ggcyto.R

library(CytoML)
library(flowWorkspace)
library(ggcyto)

xmlfile <- 'gate.xml' # Gating-ML xml file generated by Cytobank
fcsFiles <- list.files(pattern='.fcs', path='./FCS/', full.names=TRUE)
gs <- cytobank2GatingSet(xmlfile, fcsFiles)
fs <- getData(gs, "P1") # FCS file object filtered by P1 gate (live cell)
P2 <- getGate(gs, "P2") # P2 gate object (EGFP gate)

g <- ggcyto(fs, aes(y=`FSC-A`, x=`FITC-A`)) +
    facet_wrap(~name) +
    geom_hex(bins=128) +
    geom_gate(P2) +
    geom_stats(fill='transparent', digits=1.0, size=2, adjust=0.8) +
    theme_bw() +
    theme(
    	strip.background=element_rect(colour=NA, fill=NA),
    	panel.grid.major=element_blank(), aspect.ratio=1) +
    labs(x='EGFP intensity', y='FSC-A') +
    scale_y_continuous(limits=c(0, 200000))