Good morning everybody,
I am a new user and I am happy to be now part of this community ^^
I am haiving issues on how to add the adjusted pvalues (after the bonferroni correction) on top of the boxplot (using the packages ggplot2 and ggpubr) for the statistical significance.
My actual code is:
plot_Gaba + stat_compare_means(comparisons = comparison, label.y = c(8,10,12), symnum.args = signif, test = "kruskal.test", size = 5.5, p.adjust.methods = "bonferroni")
plot_Gaba includes all the codes for boxplot. I don't think is useful to report it entirely here but I can do that if you want
comparison is this: comparison <- list(c("Control", "treated1"), c("Control", "treated2"), c("treated1", "treated2")) It basically defines how to do the pairwise comparison
signif: signif <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("", "", "**", "", "ns")) It transforms the pvalues in asterisks
The above code works but it reports the original pvalues (as asterisks) from the pairwise comparison without taking into account the bonferroni correction... This is quite annoying...
Do you have any suggestion?