Easily add significance bars to your ggplots
This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown with a by a bar on top connecting the groups of interest which itself is annoted with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif) that takes the groups for comparison and the test (t.test, wilcox etc.) and adds the annotation to the plot.
Install package
install.packages("ggsignif")
# Or for the latest development version
devtools::install_github("const-ae/ggsignif")
Plot significance
library(ggplot2)
library(ggsignif)
ggplot(mpg, aes(class, hwy)) +
geom_boxplot() +
geom_signif(comparisons = list(c("compact", "midsize"), c("minivan", "suv")),
map_signif_level = TRUE, textsize=6) +
ylim(NA, 48)
Setting the precise location
This is important if you use position="dogde"
, because in that case I cannot calculate the correct position of the bars automatically.
# Calculate annotation
anno <- t.test(iris[iris$Petal.Width > 1 & iris$Species == "versicolor", "Sepal.Width"],
iris[iris$Species == "virginica", "Sepal.Width"])$p.value
# Make plot with custom x and y position of the bracket
ggplot(iris, aes(x=Species, y=Sepal.Width, fill=Petal.Width > 1)) +
geom_boxplot(position="dodge") +
geom_signif(annotation=formatC(anno, digits=1),
y_position=4.05, xmin=2.2, xmax=3,
tip_length = c(0.2, 0.04))
Advanced Example
Sometimes one needs to have a very fine tuned ability to set the location of the the significance bars in combination with facet_wrap
or facet_grid
. In those cases it you can set the flag manual=TRUE
and provide the annoations as a data.frame:
annotation_df <- data.frame(color=c("E", "H"),
start=c("Good", "Fair"),
end=c("Very Good", "Good"),
y=c(3.6, 4.7),
label=c("Comp. 1", "Comp. 2"))
annotation_df
#> color start end y label
#> 1 E Good Very Good 3.6 Comp. 1
#> 2 H Fair Good 4.7 Comp. 2
ggplot(diamonds, aes(x=cut, y=carat)) +
geom_boxplot() +
geom_signif(data=annotation_df,
aes(xmin=start, xmax=end, annotations=label, y_position=y),
textsize = 3, vjust = -0.2,
manual=TRUE) +
facet_wrap(~ color) +
ylim(NA, 5.3)
You can ignore the warning about the missing aesthetics.
For further details go the CRAN page and check the examples in the vignette.