Create a Manhattan plot of T1D GWAS statistics downloaded from T1DBase

T1DManhattan.R

## download https://www.t1dbase.org/downloads/protected_data/GWAS_Data/hg19_gwas_t1d_barrett_4_18_0.gz
## you will need to create a login!
## Then...
x <- read.table("hg19_gwas_t1d_barrett_4_18_0.gz",sep="\t",skip=1,as.is=TRUE)
colnames(x) <- c("snp","Chr","Pos","PValue","OR","kk")

## libraries
library(ggplot2)
library(cowplot) # nicer ggplot theme

x$Chr <- as.numeric(x$Chr)
x <- x[order(x$Chr,x$Pos),]
x$newchr <- c(0,diff(x$chr))
x$dPos <- c(x$Pos[1],diff(x$Pos))
x$dPos[ x$dPos < 0 ] <- 1000
x$cpos <- cumsum(x$dPos)
x$logp <- pmin(-log10(x$PValue),20)

## one way to get a two tone image is to substitute *Chr* in the line
## marked *** below with *odd*
x$odd <- as.numeric(x$Chr) %% 2
x$odd <- as.character(x$odd)

x$chrlabel <- ifelse(c(1,diff(x$Chr))==0,"",x$Chr)
x$chrx <- ifelse(x$chrlabel=="",NA,x$cpos)

g <- ggplot(x,aes(x=cpos,y=logp,col=as.factor(Chr))) + # ***
    geom_point(size=1) +
  scale_x_continuous("Chromosome",breaks=x$cpos[x$chrlabel!=""],
                     labels=x$chrlabel[x$chrlabel!=""]) +
  theme(legend.position="none",axis.text.x=element_text(angle=90),
                       text=element_text(size=16)) +
    xlab("") + ylab("Evidence for association")
g

ggsave(g, file="T1DManhattan-JDRF.jpg",height=4.67,width=12.8)
message("DONE")