rgManQQtest1
R log follows below
Loading required package: reshape
Loading required package: plyr
Attaching package: 'reshape'
The following object(s) are masked from 'package:plyr':
rename, round_any
Loading required package: grid
Loading required package: proto
[1] "### 101 values read from /data/tmp/tmpNaxDwH/database/files/000/dataset_1.dat read - now running plots"
[1] "## qqplot on Allelep done"
[1] "## manhattan on Allelep starting 2 3 8"
[1] "## manhattan plot on Allelep done"
## R script=
# generalised so 3 core fields passed as parameters ross lazarus March 24 2010 for rgenetics
# Originally created as qqman with the following
# attribution:
#--------------
# Stephen Turner
# http://StephenTurner.us/
# http://GettingGeneticsDone.blogspot.com/
# Last updated: 19 July 2011 by Ross Lazarus
# R code for making manhattan plots and QQ plots from plink output files.
# With GWAS data this can take a lot of memory. Recommended for use on
# 64bit machines only, for now.
#
library(ggplot2)
coloursTouse = c('firebrick','darkblue','goldenrod','darkgreen')
# not too ugly but need a colour expert please...
DrawManhattan = function(pvals=Null,chrom=Null,offset=Null,title=NULL, max.y="max",suggestiveline=0, genomewide=T, size.x.labels=9,
size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) {
if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!")
genomewideline=NULL # was genomewideline=-log10(5e-8)
n = length(pvals)
if (genomewide) { # use bonferroni since might be only a small region?
genomewideline = -log10(0.05/n) }
offset = as.integer(offset)
if (n > 1000000) { offset = offset/10000 }
else if (n > 10000) { offset = offset/1000}
chro = as.integer(chrom) # already dealt with X and friends?
pvals = as.double(pvals)
d=data.frame(CHR=chro,BP=offset,P=pvals)
if ("CHR" %in% names(d) & "BP" %in% names(d) & "P" %in% names(d) ) {
d=d[!is.na(d$P), ]
d=d[!is.na(d$BP), ]
d=d[!is.na(d$CHR), ]
#limit to only chrs 1-22, x=23,y=24,Mt=25?
d=d[d$CHR %in% 1:25, ]
d=d[d$P>0 & d$P<=1, ]
d$logp = as.double(-log10(d$P))
dlen = length(d$P)
d$pos=NA
ticks=NULL
lastbase=0
chrlist = unique(d$CHR)
chrlist = as.integer(chrlist)
chrlist = sort(chrlist) # returns lexical ordering
if (max.y=="max") { maxy = ceiling(max(d$logp)) }
else { maxy = max.y }
nchr = length(chrlist) # may be any number?
maxy = max(maxy,1.1*genomewideline)
if (nchr >= 2) {
for (x in c(1:nchr)) {
i = chrlist[x] # need the chrom number - may not == index
if (x == 1) { # first time
d[d$CHR==i, ]$pos = d[d$CHR==i, ]$BP # initialize to first BP of chr1
dsub = subset(d,CHR==i)
dlen = length(dsub$P)
lastbase = max(dsub$pos) # last one
tks = d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1]
lastchr = i
} else {
d[d$CHR==i, ]$pos = d[d$CHR==i, ]$BP+lastbase # one humongous contig
if (sum(is.na(lastchr),is.na(lastbase),is.na(d[d$CHR==i, ]$pos))) {
cat(paste('manhattan: For',title,'chrlistx=',i,'lastchr=',lastchr,'lastbase=',lastbase,'pos=',d[d$CHR==i,]$pos))
}
tks=c(tks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1])
lastchr = i
dsub = subset(d,CHR==i)
lastbase = max(dsub$pos) # last one
}
ticklim=c(min(d$pos),max(d$pos))
xlabs = chrlist
}
} else { # nchr is 1
nticks = 10
last = max(d$BP)
first = min(d$BP)
tks = c(first)
t = (last-first)/nticks # units per tick
for (x in c(1:(nticks))) {
tks = c(tks,round(x*t)+first) }
ticklim = c(first,last)
} # else
if (grey) {mycols=rep(c("gray10","gray60"),max(d$CHR))
} else {
mycols=rep(coloursTouse,max(d$CHR))
}
dlen = length(d$P)
d$pranks = rank(d$P)/dlen
d$centiles = 100*d$pranks # small are interesting
d$sizes = ifelse((d$centile < 1),2,1)
if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ]
if (nchr >= 2) {
manplot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR),size=factor(sizes))
manplot=manplot+scale_x_continuous(name="Chromosome", breaks=tks, labels=xlabs,limits=ticklim)
manplot=manplot+scale_size_manual(values = c(0.5,1.5)) # requires discreet scale - eg factor
#manplot=manplot+scale_size(values=c(0.5,2)) # requires continuous
}
else {
manplot=qplot(BP,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR))
manplot=manplot+scale_x_continuous(name=paste("Chromosome",chrlist[1]), breaks=tks, labels=tks,limits=ticklim)
}
manplot=manplot+scale_y_continuous(limits=c(0,maxy), breaks=1:maxy, labels=1:maxy)
manplot=manplot+scale_colour_manual(value=mycols)
if (annotate) { manplot=manplot + geom_point(data=d.annotate, colour=I("green3")) }
manplot=manplot + opts(legend.position = "none")
manplot=manplot + opts(title=title)
manplot=manplot+opts(
panel.background=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) manplot=manplot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3))
if (genomewideline) manplot=manplot+geom_hline(yintercept=genomewideline,colour="red")
manplot
} else {
stop("Make sure your data frame contains columns CHR, BP, and P")
}
}
qq = function(pvector, title=NULL, spartan=F) {
# Thanks to Daniel Shriner at NHGRI for providing this code for creating expected and observed values
o = -log10(sort(pvector,decreasing=F))
e = -log10( 1:length(o)/length(o) )
# you could use base graphics
# plot(e,o,pch=19,cex=0.25, xlab=expression(Expected~~-log[10](italic(p))),
# ylab=expression(Observed~~-log[10](italic(p))), xlim=c(0,max(e)), ylim=c(0,max(e)))
# lines(e,e,col="red")
#You'll need ggplot2 installed to do the rest
qq=qplot(e,o, xlim=c(0,max(e)), ylim=c(0,max(o))) + stat_abline(intercept=0,slope=1, col="red")
qq=qq+opts(title=title)
qq=qq+scale_x_continuous(name=expression(Expected~~-log[10](italic(p))))
qq=qq+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())
qq
}
rgqqMan = function(infile="/data/tmp/tmpNaxDwH/database/files/000/dataset_1.dat",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(8),
title="rgManQQtest1",grey=0) {
rawd = read.table(infile,head=T,sep='\t')
dn = names(rawd)
cc = dn[chromcolumn]
oc = dn[offsetcolumn]
rawd[,cc] = sub('chr','',rawd[,cc],ignore.case = T) # just in case
rawd[,cc] = sub(':','',rawd[,cc],ignore.case = T) # ugh
rawd[,cc] = sub('X',23,rawd[,cc],ignore.case = T)
rawd[,cc] = sub('Y',24,rawd[,cc],ignore.case = T)
rawd[,cc] = sub('Mt',25,rawd[,cc], ignore.case = T)
nams = c(cc,oc) # for sorting
plen = length(rawd[,1])
print(paste('###',plen,'values read from',infile,'read - now running plots',sep=' '))
rawd = rawd[do.call(order,rawd[nams]),]
# mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according.html
# in case not yet ordered
if (plen > 0) {
for (pvalscolumn in pvalscolumns) {
if (pvalscolumn > 0)
{
cname = names(rawd)[pvalscolumn]
mytitle = paste('p=',cname,', ',title,sep='')
myfname = chartr(' ','_',cname)
myqqplot = qq(rawd[,pvalscolumn],title=mytitle)
ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=6,dpi=96)
ggsave(filename=paste(myfname,"qqplot.pdf",sep='_'),myqqplot,width=8,height=6,dpi=96)
print(paste('## qqplot on',cname,'done'))
if ((chromcolumn > 0) & (offsetcolumn > 0)) {
print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn))
mymanplot= DrawManhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey)
ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=8,height=6,dpi=96)
ggsave(filename=paste(myfname,"manhattan.pdf",sep='_'),mymanplot,width=8,height=6,dpi=96)
print(paste('## manhattan plot on',cname,'done'))
}
else {
print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn,
'so no Manhattan plot - supply both chromosome and offset as numerics for Manhattan plots if required'))
}
}
else {
print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible'))
}
} # for pvalscolumn
} else { print('## Problem - no values available to plot - was there really a chromosome and offset column?') }
}
rgqqMan()
# execute with defaults as substituted
Rgenetics tool rgManQQ.py run at 04/08/2011 11:46:22