smargell/ggsignif

Easily add significance brackets to your ggplots

ggsignif

Easily add significance bars to your ggplots

Description

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.

Example

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.