Simple case

First step: load the needed packages.

library(ggplot2)
library(ggsignif)

Second step: plot your data.

ggplot(iris, aes(x = Species, y = Sepal.Length)) +
  geom_boxplot() + # using `ggsignif` to display comparison of interest
  geom_signif(
    comparisons = list(c("versicolor", "virginica")),
    map_signif_level = TRUE
  )

That’s it, it is as simple as that!

Note that, if we were to statistically analyze this data, we would run a one-way ANOVA to assess if any of the group means differ from each other and then follow up with post hoc multiple comparisons to do more fine-grained comparisons between different levels of the group. The ggsignif package provides a way to graphically display all or a few (depending on the research hypotheses context) of such comparisons.

Advanced options

Sometimes one might need more advanced control over the display. For example, instead of a one-way ANOVA design, you can have a complex multiway-ANOVA design. In such instances, you may wish to have a much finer control over which comparisons to include for pairwise comparison displays.

To specify exactly where the bracket is drawn use the y_position, xmin and xmax parameters combined with a custom annotations. This is always necessary if geom_signif is combined with another layer that uses position="dodge", because it changes the location of the visual elements without updating the data.

dat <- data.frame(
  Group = c("S1", "S1", "S2", "S2"),
  Sub = c("A", "B", "A", "B"),
  Value = c(3, 5, 7, 8)
)

ggplot(dat, aes(Group, Value)) +
  geom_bar(aes(fill = Sub), stat = "identity", position = "dodge", width = .5) +
  geom_signif(
    y_position = c(5.3, 8.3), xmin = c(0.8, 1.8), xmax = c(1.2, 2.2),
    annotation = c("**", "NS"), tip_length = 0
  ) +
  geom_signif(
    comparisons = list(c("S1", "S2")),
    y_position = 9.3, tip_length = 0, vjust = 0.2
  ) +
  scale_fill_manual(values = c("grey80", "grey20"))

For more detailed documentation of the available parameters see the manual page for the geom_signif function: https://const-ae.github.io/ggsignif/reference/stat_signif.html