Shading a kernel density plot between two points.

Question

I frequently use kernel density plots to illustrate distributions. These are easy and fast to create in R like so:

set.seed(1) draws <- rnorm(100)^2 dens <- density(draws) plot(dens) #or in one line like this: plot(density(rnorm(100)^2)) 

Which gives me this nice little PDF:

I'd like to shade the area under the PDF from the 75th to 95th percentiles. It's easy to calculate the points using the quantile function:

q75 <- quantile(draws, .75) q95 <- quantile(draws, .95) 

But how do I shade the the area between q75 and q95?

Answer 1

With the polygon() function, see its help page and I believe we had similar questions here too.

You need to find the index of the quantile values to get the actual (x,y) pairs.

Edit: Here you go:

x1 <- min(which(dens$x >= q75))   x2 <- max(which(dens$x <  q95)) with(dens, polygon(x=c(x[c(x1,x1:x2,x2)]), y= c(0, y[x1:x2], 0), col="gray")) 

Output (added by JDL)

Answer 2

Another solution:

dd <- with(dens,data.frame(x,y))  library(ggplot2)  qplot(x,y,data=dd,geom="line")+   geom_ribbon(data=subset(dd,x>q75 & x<q95),aes(ymax=y),ymin=0,               fill="red",colour=NA,alpha=0.5) 

Result: