Hi Biostar,

I have difficulty when trying to annotate pairwise p value from limma. Would you please have a suggestion? This code will annotate all boxplot the same value (0.01, 0.02, 0.03).

ggplot(long_data, aes(x = state, y = Score, fill = state)) +
  geom_boxplot() +
  facet_wrap(~ Pathway, scales = "free_y", ncol = 4) +  # Adjust scales and ncol as needed
  labs(title = "", x = "Disease state", y = "Pathway Score") +
  theme_light() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1),  # Rotate x-axis text for readability
        strip.text.x = element_text(size = 10)) +  # Adjust size of facet labels if needed
  geom_text(aes(x = Inf, y = 0.9, label = annotation_text),
            hjust = 1.1, vjust = 2, size = 4, colour = "red", inherit.aes = FALSE) +
  geom_signif(
  annotations = c("0.01", "0.02",'0.03'),
  comparisons = list(c("LS", "NC"), c("ES", "NC"), c('ES',"LS")),
  y_position  = c(0.3,0.4,0.5))

long_data from pivot_longer()
Thank you so much!

Update: stat_pvalue_manual() in ggboxplot() from library(ggpubr) worked!