CODEWITHSUNDEEP
rgraphggplot2statisticspairwise
J.Con
J.Con

Reputation: 4309

Multiple comparisons with geom_signif function, R

The package ggsignif is very useful for quickly and easily indicating significant comparisons in ggplot graphs. However the comparisons call requires manual typing of each pair of values to be compared.

Eg.

library(ggplot2)
library(ggsignif)

data(iris)

ggplot(iris, aes(x=Species, y=Sepal.Length)) + 
  geom_boxplot() +
  geom_signif(comparisons = list(c("versicolor", "virginica"),c('versicolor','setosa')), 
              map_signif_level=TRUE)

enter image description here

I'm wondering how this could be circumvented by referring to all the possible combinations at once? For example, expand.grid(x = levels(iris$Species), y = levels(iris$Species)), gives all the combinations 

           x          y
1     setosa     setosa
2 versicolor     setosa
3  virginica     setosa
4     setosa versicolor
5 versicolor versicolor
6  virginica versicolor
7     setosa  virginica
8 versicolor  virginica
9  virginica  virginica

But how to have this accepted by geom_signif(comparisons=...?

Package info is available here https://cran.r-project.org/web/packages/ggsignif/index.html

Upvotes: 4

Views: 15597

Answers (1)

erc
erc

Reputation: 10131

Building on the comment of Adam Quek you just need to transpose the created matrix and turn each row into a list:

split(t(combn(levels(iris$Species), 2)), seq(nrow(t(combn(levels(iris$Species), 2)))))

$`1`
[1] "setosa"     "versicolor"

$`2`
[1] "setosa"    "virginica"

$`3`
[1] "versicolor" "virginica" 

ggplot(iris, aes(x = Species, y = Sepal.Length)) + 
  geom_boxplot() +
  geom_signif(comparisons = split(t(combn(levels(iris$Species), 2)), seq(nrow(t(combn(levels(iris$Species), 2))))), 
              map_signif_level = TRUE)

enter image description here

Upvotes: 5

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