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manhattan_ticks.R
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manhattan_ticks.R
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# Original manhattan code forked from:
# Stephen Turner
# http://StephenTurner.us/
# http://GettingGeneticsDone.blogspot.com/
# See license at http://gettinggeneticsdone.blogspot.com/p/copyright.html
# Last updated: Tuesday, April 19, 2011
# R code for making manhattan plots and QQ plots from plink output files.
# manhattan() with GWAS data this can take a lot of memory, recommended for use on 64bit machines only, for now.
# Altnernatively, use bmanhattan() , i.e., base manhattan. uses base graphics. way faster.
## This is for testing purposes.
# set.seed(42)
# nchr=23
# nsnps=1000
# d=data.frame(
# SNP=sapply(1:(nchr*nsnps), function(x) paste("rs",x,sep='')),
# CHR=rep(1:nchr,each=nsnps),
# BP=rep(1:nsnps,nchr),
# P=runif(nchr*nsnps)
# )
# annotatesnps <- d$SNP[7550:7750]
#plot all of Achilleas cis-eQTL data files
achilleas_all <- function(flag='', file_type='jpeg', ymin=3, onepage=FALSE, filetype='jpeg', ymax=15, genomewideline=T, pca=F, exon=NULL, cis=NULL, ...){
pcaflag = ''
if (pca){
pcaflag = '_pcaCorrected'
}
datafolder = paste0("/home/jkb4y/ubs/work/data/Achilleas/eQTLs_Feb2013", pcaflag)
outfolder = paste0("/home/jkb4y/cphgdesk_share/Achilleas/eQTLs_Feb2013", pcaflag)
draw = TRUE
both = c(TRUE,FALSE)
if (is.null(cis)){
cislist = both}
else {cislist = c(cis)}
if (is.null(exon)){
exonlist = both}
else {exonlist = c(exon)}
#if (onepage){
# draw=FALSE
#base_out_loc =file.path("/home/jkb4y/ubs/work/results/Achilleas","cis_trans_Manhattans")
# base_out_loc =file.path("/home/jkb4y/cphgdesk_share/Achilleas/eQTLs_Feb2013/","Manhattans","all_Manhattans")
# if (filetype== 'jpeg'){
# jpg_out_loc = paste0(base_out_loc,".jpeg")
# jpeg(jpg_out_loc, width=1100, height=850, quality=100, title="Manhattan Plots")
# }
# else if (filetype == 'ps'){
# ps_out_loc = paste0(base_out_loc,".ps")
# postscript(file=ps_out_loc, paper="letter", horizontal=F, title="Manhattan Plots")
# }
# par(mfcol=c(5,2),mar=c(3.1,4.1,2.1,2.1))
#}
cisp = -log10(0.05/1114)
transp = -log10(0.05/54821)
for (exon in exonlist){
if (onepage){
if (exon){title_flag = 'Exon'}
else {title_flag = 'Transcript'}
draw=FALSE
#base_out_loc =file.path("/home/jkb4y/ubs/work/results/Achilleas","cis_trans_Manhattans")
base_out_loc =file.path(outfolder,"Manhattans","all_Manhattans")
if (filetype== 'jpeg'){
jpg_out_loc = paste0(base_out_loc,title_flag,".jpeg")
jpeg(jpg_out_loc, width=1100, height=850, quality=100, title=paste(title_flag,"Manhattan Plots"))
}
else if (filetype == 'ps'){
ps_out_loc = paste0(base_out_loc,title_flag,".ps")
postscript(file=ps_out_loc, paper="letter", horizontal=F, title=paste(title_flag,"Manhattan Plots"))
}
par(mfcol=c(5,2),mar=c(3.1,4.1,2.1,2.1))
}
for (cell_type in c("B","CD4","CD8","MONO","NK")){
for (cis in cislist){
if (! exon){ ymin = 2}
else {ymin = 3}
if (genomewideline!=F){
if (cis){
genomewideline=cisp}
else {genomewideline=transp}
}
print(ymin)
achilleas_eqtl_draw(cell_type=cell_type,exon=exon, cis=cis, flag=flag, ymax=ymax, draw=draw, ymin=ymin, datafolder=datafolder, genomewideline=genomewideline, outfolder=outfolder,...)
}
}
if (onepage){
dev.off()
}
}
}
# plot Achilleas' EQTL data, taking a perm flag if it is a perm file
achilleas_eqtl_draw <-function(cell_type = NULL, exon = FALSE, cis = TRUE, flag = NULL, file_type = 'jpeg',colors=c("navy","darkorange"), draw=TRUE, ymin=0, datafolder= NA, genomewideline=T,outfolder=NA,...){
filter_label = ''
if (exon){
exonflag = 'exon'
exonlabel = 'Exon'
filter_label = '_filtered_1e-04'
}
else {
exonflag = 'transcript'
exonlabel = 'Transcript'
filter_label = '_filtered_1e-02'
}
if (cis){
cislabel = 'Cis'
cisflag = 'cis'
#filter_label = ''
}
else{
cislabel = 'Trans'
cisflag = 'trans'
}
data_name = paste0(exonflag,cislabel,cell_type, filter_label,'_manhattan.txt')
#if (exon==TRUE){
# arrayflag = 'exon'
# data_name = paste0(cell_type,'_exon_cis_eqtl',permflag,'_results_noNA_JB.txt')
# arraytitle = 'Exon'
# }
#data_name = paste0(cell_type,'_cis_transcript_eqtls',permflag,'_all_new_JB.txt')
data_loc = file.path(datafolder, data_name)
print(data_loc)
#out_folder =file.path("/home/jkb4y/cphgdesk_share/Achilleas/eQTLs_Jan2013",exonflag,cisflag,cell_type,"Manhattans")
out_folder = file.path(outfolder,"Manhattans_test")
if (! file.exists(out_folder)){
dir.create(out_folder)
}
out_name_base = paste0(cell_type,"_",exonflag,"_",cisflag,"_eqtls")
pdf_out_name = paste0(out_name_base,'.pdf')
pdf_out_loc = file.path(out_folder, pdf_out_name)
png_out_loc = file.path(out_folder, paste0(out_name_base,'.png'))
ps_out_loc = file.path(out_folder, paste0(out_name_base,'.ps'))
jpg_out_loc = file.path(out_folder, paste0(out_name_base,'.jpeg'))
#out_loc = file.path(out_folder, out_name)
print('Draw is')
print(draw)
if (draw){ print("Draw is")
print(draw)
}
title = paste(cell_type,"Cells:",exonlabel,cislabel,"eQTLs")
results <- read.table(data_loc, header=T, stringsAsFactors=F)
#if (! cis & ! exon){
#if (genomewideline == F){
#threshold = 10 ^ (-1*(ymin +1))
#}
#else {threshold = 10 ^ (-1*(genomewideline -1))}
#results <- alter_table(results, threshold=threshold)
#print(head(results))
#}
#if (! exon){
#results <- read.table(data_loc, T)
#}
#else{results <- read.table(data_loc, T)}
#print(tail(results))
#postscript(file=ps_out_loc, paper="letter", horizontal=T, title=title)
#pdf(out_loc, title=title, width=11, height=8.5) #,paper="letter", horizontal=T)
#png(png_out_loc, quality=100)
if (file_type == 'ps' & draw){
#print(tail(results))
postscript(file=ps_out_loc, paper="letter", horizontal=T, title=title)
}
else if (file_type == 'pdf' & draw){
pdf(pdf_out_loc, title=title, width=11, height=8.5) #,paper="letter", horizontal=T)
}
else if (file_type == 'png' & draw) {
png(png_out_loc, quality=100)
}
else if (file_type == 'jpeg' & draw){
jpeg(jpg_out_loc, width=1100, height=850, quality=100)
}
print(title)
manhattan(results, colors=colors, main=title, suggestiveline=F, genomewideline=genomewideline, pch=16, limitchromosomes=1:23,ymin=ymin,...)
if (draw){
dev.off()
}
}
# plot Achilleas' trans-EQTL data
achilleas_trans_acting <-function(cell_type = NULL, flag = NULL, file_type = 'jpeg',colors=c("navy","darkorange"), genomewideline=F,ymin=0,draw=TRUE, data_folder,...){
#data_folder = "/home/jkb4y/ubs/work/data/Achilleas/transcript_eqtl_results_Oct12"
data_name = paste0(cell_type,'')
data_loc = file.path(data_folder, data_name)
print(data_loc)
out_folder =file.path("/home/jkb4y/ubs/work/results/Achilleas/transcript_eqtl_results_Oct12",cell_type,"Manhattans")
if (! file.exists(out_folder)){
dir.create(out_folder)
}
if (is.null(flag)) { addflag=''}
else{ addflag = paste0('_',flag)}
pdf_out_name = paste0(cell_type, "_trans_eqtls",addflag,".pdf")
pdf_out_loc = file.path(out_folder, pdf_out_name)
png_out_loc = file.path(out_folder, paste0(cell_type, "_trans_eqtls",addflag,".png"))
ps_out_loc = file.path(out_folder, paste0(cell_type, "_trans_eqtls",addflag,".ps"))
jpg_out_loc = file.path(out_folder, paste0(cell_type, "_trans_eqtls",addflag,".jpeg"))
title = paste(cell_type,"Cells: Trans eQTLs")
results <- read.table(data_loc, T)
results <- results[results$TRANS.CIS == "trans", ]
print(head(results))
if (file_type == 'ps' & draw){
#print(tail(results))
postscript(file=ps_out_loc, paper="letter", horizontal=T, title=title)
}
else if (file_type == 'pdf' & draw){
pdf(pdf_out_loc, title=title, width=11, height=8.5) #,paper="letter", horizontal=T)
}
else if (file_type == 'png' & draw) {
png(png_out_loc, quality=100)
}
else if (file_type == 'jpeg' & draw){
jpeg(jpg_out_loc, width=1100, height=850, quality=100)
}
manhattan(results, colors=colors, main=title, suggestiveline=F, genomewideline=genomewideline, pch=16, limitchromosomes=1:23,ymin=ymin, ...)
if (draw){
dev.off()
}
}
#function to alter the table to be drawable within the human lifespan
alter_table <- function(df, threshold){
library('plyr')
snp.list <- unique(df$SNP)
subtable <- ldply(snp.list,.fun=function(x){alter_helper(as.character(x), df, threshold)})
return(subtable)
}
#helper function
alter_helper <-function(snp, df, threshold){
sub = df[as.character(df$SNP)==as.character(snp), ]
#print(nrow(sub))
top = as.numeric(sub$P[order(sub$P)[1]])
bottom = as.numeric(sub$P[order(sub$P)[nrow(sub)]])
sub = sub[as.numeric(sub$P) < as.numeric(threshold) | as.numeric(sub$P) == top,]
#print(sub)
#print(top)
#print(nrow(sub))
#print(threshold)
return(sub)
}
# manhattan plot using base graphics
manhattan <- function(dataframe, colors=c("navy","darkorange"), ymax="max", limitchromosomes=1:23,
suggestiveline=F, genomewideline=F, annotate=NULL, ymin=0,...) {
#suggestiveline=-log10(1e-5), genomewideline=-log10(5e-8), annotate=NULL, ...) {
d=dataframe
#print(names(d))
if (!("CHR" %in% names(d) & "BP" %in% names(d) )) stop("Make sure your data frame contains columns CHR and BP")
if (!("P" %in% names(d) | "EMP1" %in% names(d))) stop("Make sure your data frame contains EITHER column P or column EMP1")
if("EMP1" %in% names(d)) d$P = d$EMP1;
if (any(limitchromosomes)) d=d[d$CHR %in% limitchromosomes, ]
if (ymin == 0){
pmax = 1}
else{
pmax = 10^-(ymin)
}
d=subset(na.omit(d[order(d$CHR, d$BP), ]), (P>0 & P<=pmax)) # remove na's, sort, and keep only 0<P<=1
d$logp = -log10(d$P)
d$pos=NA
ticks=NULL
lastbase=0
colors <- rep(colors,max(d$CHR))[1:max(d$CHR)]
if (ymax=="max") ymax<-ceiling(max(d$logp))
if (ymax<8) ymax<-8
numchroms=length(unique(d$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)$BP, 1)
#print(lastbase)
d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP+lastbase
}
ordered = order(d[d$CHR==i,]$BP)
len = length(ordered)
first <- as.numeric(d[d$CHR==i,]$pos[ ordered[1] ]);
last <- as.numeric(d[d$CHR==i,]$pos[ ordered[len]] );
mid = (last - first)/2
middle = first + mid
#print(c(first, last, middle))
ordered = NULL
ticks=c(ticks, middle)
#ticks=c(ticks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1])
#print(ticks)
}
}
if (numchroms==1) {
#with(d, plot(pos, logp, ylim=c(ymin,ymax), ylab=expression(-log[10](italic(p))), xlab=paste("Chromosome",unique(d$CHR),"position"), ...))
with(d, plot(pos, logp, ylim=c(ymin,ymax), ylab=expression(-log[10](p)), xlab=paste("Chromosome",unique(d$CHR),"position"), ...))
} else {
#with(d, plot(pos, logp, ylim=c(ymin,ymax), ylab=expression(-log[10](italic(p))), xlab="Chromosome", xaxt="n", type="n", ...))
with(d, plot(pos, logp, ylim=c(ymin,ymax), ylab=expression(-log[10](p)), xlab="Chromosome", xaxt="n", type="n", ...))
axis(1, at=ticks, lab=unique(d$CHR), ...)
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(annotate)) {
d.annotate=d[which(d$SNP %in% annotate), ]
with(d.annotate, points(pos, logp, col="green3", ...))
}
if (suggestiveline) abline(h=suggestiveline, col="blue")
if (genomewideline) abline(h=genomewideline, col="red")
}
## Make a pretty QQ plot of p-values
qq = function(pvector, ...) {
if (!is.numeric(pvector)) stop("D'oh! P value vector is not numeric.")
pvector <- pvector[!is.na(pvector) & pvector<1 & pvector>0]
o = -log10(sort(pvector,decreasing=F))
e = -log10( ppoints(length(pvector) ))
plot(e,o,pch=19,cex=1, xlab=expression(Expected~~-log[10](italic(p))), ylab=expression(Observed~~-log[10](italic(p))), xlim=c(0,max(e)), ylim=c(0,max(o)), ...)
abline(0,1,col="red")
}
## Make a pretty QQ plot of p-values
qq_jb = function(pvector, ...) {
if (!is.numeric(pvector)) stop("D'oh! P value vector is not numeric.")
pvector <- pvector[!is.na(pvector) & pvector<1 & pvector>0]
o = -log10(sort(pvector,decreasing=F))
e = -log10( ppoints(length(pvector) ))
lim_max = ceiling(max(c(e,o)))
plot(e,o,pch=19,cex=1, xlab=expression(Expected~~-log[10](p)), ylab=expression(Observed~~-log[10](p)), xlim=c(0,lim_max), ylim=c(0,lim_max),xaxs='i',yaxs='i', ...)
abline(0,1,col="red")
}
### OLD GGPLOT2 CODE ###
# manhattan plot using ggplot2
gg.manhattan = function(dataframe, title=NULL, max.y="max", suggestiveline=0, genomewideline=-log10(5e-8), size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL) {
library(ggplot2)
if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!")
d=dataframe
#limit to only chrs 1-23?
d=d[d$CHR %in% 1:23, ]
if ("CHR" %in% names(d) & "BP" %in% names(d) & "P" %in% names(d) ) {
d=na.omit(d)
d=d[d$P>0 & d$P<=1, ]
d$logp = -log10(d$P)
d$pos=NA
ticks=NULL
lastbase=0
#new 2010-05-10
numchroms=length(unique(d$CHR))
if (numchroms==1) {
d$pos=d$BP
} 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])
}
ticklim=c(min(d$pos),max(d$pos))
}
mycols=rep(c("gray10","gray60"),max(d$CHR))
if (max.y=="max") maxy=ceiling(max(d$logp)) else maxy=max.y
if (maxy<8) maxy=8
if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ]
if (numchroms==1) {
plot=qplot(pos,logp,data=d,ylab=expression(-log[10](italic(p))), xlab=paste("Chromosome",unique(d$CHR),"position"))
} else {
plot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR))
plot=plot+scale_x_continuous(name="Chromosome", breaks=ticks, labels=(unique(d$CHR)))
plot=plot+scale_y_continuous(limits=c(0,maxy), breaks=1:maxy, labels=1:maxy)
plot=plot+scale_colour_manual(value=mycols)
}
if (annotate) plot=plot + geom_point(data=d.annotate, colour=I("green3"))
plot=plot + opts(legend.position = "none")
plot=plot + opts(title=title)
plot=plot+opts(
panel.background=theme_blank(),
panel.grid.minor=theme_blank(),
axis.text.x=theme_text(size=size.x.labels, colour="grey50"),
axis.text.y=theme_text(size=size.y.labels, colour="grey50"),
axis.ticks=theme_segment(colour=NA)
)
if (suggestiveline) plot=plot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3))
if (genomewideline) plot=plot+geom_hline(yintercept=genomewideline,colour="red")
plot
} else {
stop("Make sure your data frame contains columns CHR, BP, and P")
}
}
gg.qq = function(pvector, title=NULL, spartan=F) {
library(ggplot2)
o = -log10(sort(pvector,decreasing=F))
#e = -log10( 1:length(o)/length(o) )
e = -log10( ppoints(length(pvector) ))
plot=qplot(e,o, xlim=c(0,max(e)), ylim=c(0,max(o))) + stat_abline(intercept=0,slope=1, col="red")
plot=plot+opts(title=title)
plot=plot+scale_x_continuous(name=expression(Expected~~-log[10](italic(p))))
plot=plot+scale_y_continuous(name=expression(Observed~~-log[10](italic(p))))
if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank())
plot
}
gg.qqman = function(data="plinkresults") {
myqqplot = ggqq(data$P)
mymanplot = ggmanhattan(data)
ggsave(file="qqplot.png",myqqplot,w=5,h=5,dpi=100)
ggsave(file="manhattan.png",mymanplot,width=12,height=9,dpi=100)
}
gg.qqmanall= function(command="ls *assoc") {
filelist=system(command,intern=T)
datalist=NULL
for (i in filelist) {datalist[[i]]=read.table(i,T)}
highestneglogp=ceiling(max(sapply(datalist, function(df) max(na.omit(-log10(df$P))))))
print(paste("Highest -log10(P) = ",highestneglogp),quote=F)
start=Sys.time()
for (i in names(datalist)) {
myqqplot=ggqq(datalist[[i]]$P, title=i)
ggsave(file=paste("qqplot-", i, ".png", sep=""),myqqplot, width=5, height=5,dpi=100)
mymanplot=ggmanhattan(datalist[[i]], title=i, max.y=highestneglogp)
ggsave(file=paste("manhattan-", i, ".png", sep=""),mymanplot,width=12,height=9,dpi=100)
}
end=Sys.time()
print(elapsed<-end-start)
}