Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket 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.text() etc.) as arguments and adds the annotation to the plot.
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.
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 annotationanno <- 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 bracketggplot(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 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. 2ggplot(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.
alpha()from another package was loaded (issue #2)
The package has been made publicly available on CRAN: https://CRAN.R-project.org/package=ggsignif