Following the example in this question: R: problems plotting p-values from conover test (Dunn's works fine)
# https://stackoverflow.com/questions/61922336/r-problems-plotting-p-values-from-conover-test-dunns-works-fine
library(dplyr)
library(ggpubr)
library(rstatix)
# I'm going to get the Conover test from this package
require(DescTools)
# You didn't provide data I will use mtcars
mydata <- mtcars %>% select(mpg, gear)
mydata$gear <- factor(mydata$gear)
# Here's what you were doing
stat.test.dunn <- mydata %>% dunn_test(mpg ~ gear, p.adjust.method = "hochberg")
stat.test.dunn <- stat.test.dunn %>% add_xy_position(x = "gear")
stat.test.dunn
#> # A tibble: 3 x 13
#> .y. group1 group2 n1 n2 statistic p p.adj p.adj.signif
#> <chr> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <chr>
#> 1 mpg 3 4 15 12 3.76 1.69e-4 5.06e-4 ***
#> 2 mpg 3 5 15 5 1.65 9.98e-2 2.00e-1 ns
#> 3 mpg 4 5 12 5 -1.14 2.54e-1 2.54e-1 ns
#> # … with 4 more variables: y.position <dbl>, groups <named list>, xmin <int>,
#> # xmax <int>
ggboxplot(mydata, x = "gear", y = "mpg", fill = "gear") +
stat_pvalue_manual(stat.test.dunn, hide.ns = FALSE)
I would like to know how I can change the order of the groups on the x-axis. They are automatically sorted in alphabetical order but I don't know how to assign a specific order to the groups. Following the example, I would like the gear 4 group to appear on the left, gear 5 in the center and gear 3 on the right. And I need the p values to be assigned correctly between the groups.
I tried to arrange the table by ordering the group1 column but the result is the same. Also tried adding:
+ scale_x_discrete(limits=c("group_I_want_on_left", "group_I_want_in_center", "group_I_want_on_right"))
This does change the order of the boxes but the p values are not correct because they appear in the same order as when I had the boxes in alphabetical order.
