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 by a bar on top connecting the groups of interest which itself is annotated 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.packages("ggsignif") # Or for the latest development version devtools::install_github("const-ae/ggsignif")
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="dodge", 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))
Sometimes one needs to have a very fine tuned ability to set the location of the the significance bars in combination with
facet_grid. In those cases it you can set the flag
manual=TRUE and provide the annotations 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.
This package is provided as is and I currently don't have any plans and the capacity to add any new features to it. If there is nonetheless a feature which you would like to see in the package, you are always welcome to submit pull request, which I will try to address as soon as possible.
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