I believe this is what you want to do, though it may need tweaking.

#Make up some data
> a=seq(1,100,by=1)
> b=runif(100,0,0.5)

#Make a matrix
> matrix=cbind(a,b)

#Subset the matrix based upon values of interest
> subsetmatrix=matrix[which(b<0.1),]

#Plot values
> 
> plot(subsetmatrix[,2]~subsetmatrix[,1],ylim=c(0,1),las=1,ylab='Explan',xlab='Window')


Hope this helps. 



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