Some time ago I asked a question about drawing boxplot Link1.
I have got some data with 3 different groups (or labels) Please down load here. I can use the following
I know that this is an old question and the answer by DatamineR already provides one solution for the problem. But I recently created a ggplot-extension that simplifies the whole process of adding significance bars: ggsignif
Instead of tediously adding the geom_line and annotate to your plot you just add a single layer geom_signif:
library(ggplot2)
library(ggsignif)
ggplot(iris, aes(x=Species, y=Sepal.Length)) +
geom_boxplot() +
geom_signif(comparisons = list(c("versicolor", "virginica")),
map_signif_level=TRUE)
Full documentation of the package is available at CRAN.