mydata <- read.table("mds_components.txt",header=T)
mydata$pch[mydata$Group==1]<-15
mydata$pch[mydata$Group==2]<-16
mydata$pch[mydata$Group==3]<-2
jpeg("/home/student/Desktop/mds.jpeg",height=1000,width=1000)
plot(mydata$C1,mydata$C2,pch=mydata$pch)
dev.off()
broadqq<-function(pvals,title)
{
observed <- sort(pvals)
lobs <- -(log10(observed))
expected <- c(1:length(observed))
lexp <- -(log10(expected/(length(expected)+1)))
plot(c(0,7),c(0,7),col="red",lwd=3,type="l",xlab="Expected (-logP)",ylab="Observed (-logP)",xlim=c(0,max(lobs)),ylim=c(0,max(lobs)),las=1,xaxs="i",yaxs="i",bty="l",main=title)
points(lexp,lobs,pch=23,cex=.4,bg="black")
}
ls()
jpeg("/home/student/Desktop/qqplot_compare.jpeg",height=1000,width=1000)
par(mfrow=c(2,1))
aff_unadj<-read.table("unadj.assoc.logistic",header=T)
aff_unadj.add.p<-aff_unadj[aff_unadj$TEST==c("ADD"),]$P
broadqq(aff_unadj.add.p,"Some Train Unadjusted")
aff_C1C2<-read.table("C1-C2.assoc.logistic",header=T)
aff_C1C2.add.p<-aff_C1C2[aff_C1C2$TEST==c("ADD"),]$P
broadqq(aff_C1C2.add.p,"Some Trait Adjusted")
dev.off()
broadqq<-function(pvals,title)
{
observed <- sort(pvals)
lobs <- -(log10(observed))
expected <- c(1:length(observed))
lexp <- -(log10(expected/(length(expected)+1)))
plot(c(0,7),c(0,7),col="red",lwd=3,type="l",xlab="Expected (-logP)",ylab="Observed (-logP)",xlim=c(0,max(lexp)),ylim=c(0,max(lobs)),las=1,xaxs="i",yaxs="i",bty="l",main=title)
points(lexp,lobs,pch=23,cex=.4,bg="black")
}
jpeg("/home/student/Desktop/qqplot_compare2.jpeg",height=1000,width=1000)
par(mfrow=c(1,2))
broadqq(aff_unadj.add.p,"Some Train Unadjusted")
broadqq(aff_C1C2.add.p,"Some Trait Adjusted")
dev.off()
broadqq<-function(pvals,title)
{
observed <- sort(pvals)
lobs <- -(log10(observed))
expected <- c(1:length(observed))
lexp <- -(log10(expected/(length(expected)+1)))
plot(c(0,7),c(0,7),col="red",lwd=3,type="l",xlab="Expected (-logP)",ylab="Observed (-logP)",xlim=c(0,max(lobs)),ylim=c(0,max(lobs)),las=1,xaxs="i",yaxs="i",bty="l",main=title)
points(lexp,lobs,pch=23,cex=.4,bg="black")
}
jpeg("/home/student/Desktop/qqplot_compare2.jpeg",height=1000,width=1000)
broadqq(aff_unadj.add.p,"Some Trait Unadjusted")
broadqq(aff_C1C2.add.p,"Some Trait Adjusted")
dev.off()
gws_unadj<-aff_unadj[which(aff_unadj$P<0.0000001),]
gws_unadj
gws_adjusted<-aff_C1C2[which(aff_C1C2$P<0.0000001),]
gws_adjusted
q()
