#### in R
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("mds.jpeg", height=500, width=500)
plot(mydata$C1, mydata$C2 ,pch=mydata$pch)
broadqq <-function(pvals, title)
{
observed <- sort(pvals) lobs <- -(log10(observed)) expected <- c(1:length(observed)) lexp <- -(log10(expected / (length(expected)+1))) plot(c(0,7), c(0,7), col="red", lwd=3, type="l", xlab="Expected (-logP)", ylab="Observed (-logP)", xlim=c(0,max(lobs)), ylim=c(0,max(lobs)), las=1, xaxs="i", yaxs="i", bty="l", main = title) points(lexp, lobs, pch=23, cex=.4, bg="black") }
jpeg("qqplot_compare.jpeg", height=1000, width=500)
par(mfrow=c(2,1))
aff_unadj<-read.table("unadj.assoc.logistic", header=TRUE)
aff_unadj.add.p<-aff_unadj[[aff_unadj$TEST==c("ADD"),]]$P
broadqq(aff_unadj.add.p,"Some Trait Unadjusted")
aff_C1C2<-read.table("PC1-PC2.assoc.logistic", header=TRUE)
aff_C1C2.add.p<-aff_C1C2[[aff_C1C2$TEST==c("ADD"),]]$P
broadqq(aff_C1C2.add.p, "Some Trait Adjusted for PC1 and PC2")
dev.off()
gws_unadj = aff_unadj[[which(aff_unadj$P < < 0.0000001),]]
gws_unadj
gws_adjusted = aff_C1C2[[which(aff_C1C2$P < < 0.0000001),]] gws_adjusted ===VAT===
vtools -h
vtools init VATDemo