source("manhattan_v1.R")

ls()

gwas <- read.table(“plink.assoc”,head=T)

head(gwas)

dim(gwas)

data_to_plot <- data.frame(CHR=gwas$CHR, BP=gwas$BP, P=gwas$P)

manhattan(data_to_plot, GWthresh=5e-8, GreyZoneThresh=1e-5, DrawGWline=FALSE)

## PDF

pdf("my_first_MH_plot.pdf",width=8,height=6)
manhattan(data_to_plot, GWthresh=5e-8, GreyZoneThresh=1e-5, DrawGWline=FALSE)
dev.off()

## TIFF

tiff(filename="my_first_MH_plot.tiff",res=300,width=6, height = 3,units="in")
manhattan(data_to_plot, GWthresh=5e-8, GreyZoneThresh=1e-5, DrawGWline=FALSE)
dev.off()