ggplot2 shade area under density curve by group

by

Here is one way (and, as @joran says, this is an extension of the response here):

#  same data, just renaming columns for clarity later on
#  also, use data tables
library(data.table)
set.seed(1)
value <- c(rnorm(50, mean = 1), rnorm(50, mean = 3))
site  <- c(rep("site1", 50), rep("site2", 50))
dt    <- data.table(site,value)
#  generate kdf
gg <- dt[,list(x=density(value)$x, y=density(value)$y),by="site"]
#  calculate quantiles
q1 <- quantile(dt[site=="site1",value],0.01)
q2 <- quantile(dt[site=="site2",value],0.75)
# generate the plot
ggplot(dt) + stat_density(aes(x=value,color=site),geom="line",position="dodge")+
  geom_ribbon(data=subset(gg,site=="site1" & x>q1),
              aes(x=x,ymax=y),ymin=0,fill="red", alpha=0.5)+
  geom_ribbon(data=subset(gg,site=="site2" & x<q2),
              aes(x=x,ymax=y),ymin=0,fill="blue", alpha=0.5)

Produces this:

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