Combining a box plot with a dot plot using different Y scales - r

Question

I am trying to generate a figure that consists of a box plot with a set of points overlaid on the boxplot. The key issue is that the y scale of the box plot is different from that of the points. (Yes, this is very poor visualization - but I'm not the lead author of the paper). I have been able to generate a plot with different y scales, but am facing an issue with the x axis.
Using the following code
boxdata <- data.frame(fc=runif(100, min=-4, max=4),
sym=sample(c('A', 'B', 'C', 'D', 'E'), 100, replace=TRUE))
par(mar=c(5, 4, 1, 6) + 0.1)
junk <- boxplot(fc ~ sym, boxdata, las=2, pch=19, ylim=c(-5,5),
varwidth=FALSE, xaxt='n')
mtext("Y-axis",side=2,line=2.5)
axis(1, at=1:5, labels=sort(unique(boxdata$sym)), las=2)
par(new=TRUE)
x <- 1:5
y <- runif(5, min=-1, max=1)
plot(x,y, col='red', type='p', pch=15, axes=FALSE, ylim=c(-1,1), cex=1.5)
axis(4, ylim=c(-1,1), las=1)
I get the following figure. As you can see the points in red do not align with the X-axis labels (or box centers). The box centers are located at 1:5, so I thought that the plot() call with x = 1:5 should line up.
Could anybody point me to a way to line up the second set of points with the box centers?
EDIT: This problem doesn't occur if I plot two sets of points on different y scales
plot(1:10, runif(10) , col='red', pch=19)
par(new=TRUE)
plot(1:10, runif(10, min=5, max=20), col='blue', pch=19, axes=FALSE)
axis(4, las=2)

Answer 1

Don't use par(new=TRUE), but use pointsinstead of the second plotcommand:
boxdata <- data.frame(fc=runif(100, min=-4, max=4),
sym=sample(c('A', 'B', 'C', 'D', 'E'), 100, replace=TRUE))
par(mar=c(5, 4, 1, 6) + 0.1)
junk <- boxplot(fc ~ sym, boxdata, las=2, pch=19, ylim=c(-5,5),
varwidth=FALSE, xaxt='n')
mtext("Y-axis",side=2,line=2.5)
axis(1, at=1:5, labels=sort(unique(boxdata$sym)), las=2)
x <- 1:5
y <- runif(5, min=-1, max=1)
points(x, 4*y, col='red', type='p', pch=15, ylim=c(-1,1), cex=1.5)
axis(4, at=seq(-4, 4, by=2), label=seq(-1, 1, by=.5), las=1)
EDIT: Check the ?bxp help page. You will find a note that xlim defaults to range(at, *) + c(-0.5, 0.5). So, you could specify the same for your second plot:
junk <- boxplot(fc ~ sym, boxdata, las=2, pch=19, ylim=c(-5,5),
varwidth=FALSE, xaxt='n')
mtext("Y-axis",side=2,line=2.5)
axis(1, at=1:5, labels=sort(unique(boxdata$sym)), las=2)
par(new=TRUE)
plot(x,y, col='red', type='p', pch=15, axes=FALSE, ylim=c(-1,1), cex=1.5,
xlim=range(x) + c(-0.5, 0.5))
axis(4, ylim=c(-1,1), las=1)