Today I experimented with the good old contour plots in R. I plotted my points rather large, because there is quite some uncertainty around their precise placement. In this particular case, I start with an empty plot and a custom range, and add the points separately. Note the cex=8 to draw extra large points.
plot(c(80, 740), c(180, 740) , type='n', xlab="", ylab="", bty="n", main="")
points(jitter(x), jitter(y), cex=8, pch=19, col="#AA449950")
Then I added contours, and they were cut off, breaking off where I expected them to go around the dots. Why are there incomplete lines at the top and bottom?
It turns out — a.k.a. read the manual — that kde2d sets the default limits to the range (I guess this is quite reasonable in other cases): lims = c(range(x), range(y)). Now my big dots obviously cover more than the strict range of values, so all I needed to do was set my own lims in kde2d.
Here’s the entire code for the plot:
plot(c(80, 740), c(180, 740) , type='n', xlab="", ylab="", bty="n", main="")
points(jitter(x), jitter(y), cex=8, pch=19, col="#AA449950")
library(MASS)
# z = kde2d(x, y, n=50) # this one didn't work out
z = kde2d(x, y, n=50, lims=c(80, 740, 180, 740))
contour(z, drawlabels=FALSE, nlevels=6, col="#AA4499", add=TRUE)
Didier Ruedin 