Manhattan.R

## -- chromosome mid-points
mid <- function(x1,x2) {abs(x2-x1)/2 + min(x1,x2)}
mid2 <- function(x1,x2) {(x2-x1)/2 + x1}
mid.vec <- function(x){
  z <- vector(length=length(x)-1)
 for (i in 1:length(z)){z[i] <- mid(x[i+1],x[i])}
 return(z)
}



## --- Updated Manhattan function
manhattan <- function(dataframe, colors=c("gray10", "gray50"), ymax="max", limitchromosomes=1:23, suggestiveline=-log10(1e-5), genomewideline=-log10(5e-8), annotate=NULL, annotate2=NULL, ...) {

    d=dataframe
    if (!("CHR" %in% names(d) & "BP" %in% names(d) & "P" %in% names(d))) stop("Make sure your data frame contains columns CHR, BP, and P")
    
    if (any(limitchromosomes)) d=d[d$CHR %in% limitchromosomes, ]
    d=subset(na.omit(d[order(d$CHR, d$BP), ]), (P>0 & P<=1)) # remove na's, sort, and keep only 0<P<=1
    d$logp = -log10(d$P)
    d$pos=NA
    ticks=NULL
    lastbase=0
    colors <- rep(colors,max(d$CHR))[1:max(d$CHR)]
    if (ymax=="min") ymax<-18
    if (ymax=="max") ymax<-ceiling(max(d$logp))
    if (ymax<8) ymax<-ymax
    
    numchroms=length(unique(d$CHR))
    if (numchroms==1) {
        d$pos=d$BP
        ticks=floor(length(d$pos))/2+1
    } else {
        for (i in unique(d$CHR)) {
          if (i==1) {
    			d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP
    		} else {
    			lastbase=lastbase+tail(subset(d,CHR==i-1)$BP, 1)
    			d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP+lastbase
    		}
    		ticks=c(ticks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1])
    	}
    }
    
    if (numchroms==1) {
        with(d, plot(pos, logp, ylim=c(0,ymax), ylab=expression(-log[10](italic(p))), xlab=paste("Chromosome",unique(d$CHR),"position"), ...))
    }	else {
        with(d, plot(pos, logp, ylim=c(0,ymax), ylab=expression(-log[10](italic(p))), xlab="Chromosome", xaxt="n", type="n", ...))
        axis(1, at=mid.vec(adder), lab=c(1:22,'X'), ...)
        icol=1
        for (i in unique(d$CHR)) {
            with(d[d$CHR==i, ],points(pos, logp, col=colors[icol], ...))
            icol=icol+1
    	}
    }

    if (!is.null(annotate2)) {
        d.annotate2=d[which(d$SNP %in% annotate2), ]
        with(d.annotate2, points(pos, logp, col="chocolate", ...)) 
    }
    
    if (!is.null(annotate)) {
        d.annotate=d[which(d$SNP %in% annotate), ]
        with(d.annotate, points(pos, logp, col="green3", ...)) 
    }

    
    if (suggestiveline) abline(h=suggestiveline, col="blue")
    if (genomewideline) abline(h=genomewideline, col="red")
}