add x=y line to scatterplot

Question

I am using the scatterplot function from the car package to generate a scatterplot. I want to be able to generate a reference line in the plot that should be x=y. I tried using abline and it does add a line but it is not the x=y line. Can someone help?

My code is as follows:

scatterplot(phenos$P1~pheno$P0, data=pheno,spread=FALSE,ylab="6 month timepoint", xlab="Baseline Timepoint", jitter=list(x=1, y=1))
abline(0,1)

Thanks.

Answer 1

This is actually fairly difficult/hackish, because scatterplot() internally uses layout, which makes it hard to control the subplot currently being used by the graphics driver. (Update: it's harder than I thought -- setting par("mfg") must have been working more or less by accident.)

Make up data (update: using data with mean x and y not equal zero and not equal to each other, as it illustrate the difficulties of naively using abline() more clearly)

set.seed(1)
d <- data.frame(x=rnorm(10,mean=10),y=rnorm(10,mean=12))
library(car)

Try my old strategy (which doesn't actually work, or works only unpredictably):

scatterplot(y~x,data=d,reset.par=FALSE)
k <- 1              
for (i in 1:2) {
   for (j in 1:2) {
      par(mfg=c(i,j,2,2))
        abline(0,1,lwd=3,col=k)
        k <- k+1
  }

}

Depending on how I do this, I either get warnings and errors or bogus answers. It seems to matter whether I do the scatterplot() call inside a function ... ??

Second try, more conservatively: reconstruct layout from scratch.

 scatterplot(y~x,data=d)
 uu <- par("usr")
 ## mimic layout frolm car:::scatterplot.default.  Would be different if we were drawing only one
 ## of x-boxes or y-boxes
 layout(matrix(c(1, 0, 3, 2), 2, 2), widths = c(5, 95), 
        heights = c(95, 5))
 oldmar <- par(mar=rep(0,4))  ## zero out margins so we can plot in sub-boxes without errors
 ## now skip through the first two sub-plots
 par(new=TRUE); plot.new(); par(new=TRUE); plot.new()
 par(oldmar)  ## reset margins
 ## blank plot with user limits set and 'interior' axis calculations
 plot(0:1,0:1,xlab="",ylab="",xlim=uu[1:2],ylim=uu[3:4],xaxs="i",yaxs="i")
 ## add annotation
 abline(a=0,b=1,col=4,lwd=3)              

Given the amount of effort and fragility of this solution, it might actually be best to hack scatterplot to optionally allow abline() to be specified additionally, or to ask the maintainer for that capability ...

Answer 2

You can achieve your goal by the same function abline. Use the function abline(a=0, b=1) where a and b are the intercept and slop of the line respectively. This draws you a straight line of the form Y = a + b*x.

Hope this helps.

Answer 3

I just use the segments function: segments(x0=0,y0=0,x1=45,y1=45)

Just make the y values go just above the limits of your plot.

This function is also nice because it doesn't change your x and y limits so the line can run clean across your graph without having to accurately pick the x and y values.