Post date: Jan 07, 2017 2:27:34 AM
As with the other genomic change analyses (FHA, Ecol. Letters), I quantified excess change for 128, 702.1, 128-left and 128-right relative to diversity. All but 128-right (and particularly 128-left) really stand out as being high change, high diversity, and high change relative to diversity (mean change, 95q change). The full code is commands.R in /uufs/chpc.utah.edu/common/home/u6000989/projects/timema_fluct/genomic_change_dark_morph/popgen_oga, but the most relevant (new) excerpt is below:
pdf("ogaDiv95qChange.pdf",width=4,height=10)
par(mfrow=c(5,2))
par(mar=c(4,4,2,2))
for(i in 1:10){
a<-which(scn[[i]] > 500)
x<-cbind(scvar[[i]][a],scq95[[i]][a])
plot(x[,1],x[,2],ylim=c(0.0,0.5),xlim=c(0.1,0.18),xlab="diversity (2pq)",ylab="95 q change",cex.lab=1.1,cex.axis=1)
o<-lm(x[,2] ~ x[,1])
abline(o$coefficients)
title(main=paste(trt[i],", ",re[i]))
## scaf 128
q128[i]<-x[3,2]
points(x[3,1],x[3,2],col="blue",pch=19)
## scaf 702.1
q702[i]<-x[15,2]
points(x[15,1],x[15,2],col="red",pch=19)
## left and right
mn128l[i]<-quantile(dp[[i]][left],probs=0.95)
mn128r[i]<-quantile(dp[[i]][right],probs=0.95)
var128l<-mean(2 * p0[left] * (1-p0[left]))
var128r<-mean(2 * p0[right] * (1-p0[right]))
points(var128l,mn128l[i],col="green",pch=19)
points(var128r,mn128r[i],col="orange",pch=19)
}
for(i in 1:10){ ## residuals
a<-which(scn[[i]] > 500)
o<-lm(scq95[[i]][a] ~ scvar[[i]][a])
x<-cbind(scvar[[i]][a],o$residuals)
plot(x[,1],x[,2],ylim=c(-0.1,0.3),xlim=c(0.1,0.18),xlab="diversity (2pq)",ylab="residual change",cex.lab=1.1,cex.axis=1)
title(main=paste(trt[i],", ",re[i]))
## scaf 128
q128[i]<-x[3,2]
points(x[3,1],x[3,2],col="blue",pch=19)
## scaf 702.1
q702[i]<-x[15,2]
points(x[15,1],x[15,2],col="red",pch=19)
## left and right
mn128l[i]<-quantile(dp[[i]][left],probs=0.95)
mn128r[i]<-quantile(dp[[i]][right],probs=0.95)
var128l<-mean(2 * p0[left] * (1-p0[left]))
var128r<-mean(2 * p0[right] * (1-p0[right]))
ex<-o$coefficients[1] + o$coefficients[2] * var128l
points(var128l,mn128l[i]-ex,col="green",pch=19)
ex<-o$coefficients[1] + o$coefficients[2] * var128r
points(var128r,mn128r[i]-ex,col="orange",pch=19)
abline(h=0,lty=2)
}
dev.off()