Adding p-values to ggplot facets with different scales

Question

When I try to add p-values to multifacet ggplot with different scales, they are getting shifted, although in facet_wrap to ggplot and add_xy_position to stats I indicate scales="free":

my code chunks:

stat_c <- dat_c %>%
  group_by(antigen , region) %>%
  wilcox_test(norm_mean ~ genotype , alternative = "greater") %>%
  adjust_pvalue(method = "bonferroni") %>%
  add_significance("p.adj") %>%
  add_xy_position(x = "region" , dodge = 0.8 , scales = "free")

plt_c <- ggplot(dat_c , aes(x = region , y = norm_mean , color = genotype)) + 
  geom_boxplot(outlier.shape=NA) +
  geom_jitter(position=position_jitterdodge()) +
  facet_wrap(~antigen , scales = "free" ) +
  ggtitle(label = "DRS hit IHC in tent5c KO")

plt_c + 
  stat_pvalue_manual(stat_c , label = "p.adj") + 
  scale_y_continuous(expand = expansion(mult = c(0,0.1)))

I'd be supergrateful for any help!

Answer 1

I just ran into the same issue with some data I was working with. The trick is to calculate the pvalues for each facet independently and rbind the tables togehter. This way the x-values for each facet are derived independently. Your solution may look something like this:

antigens = levels(factor(dat_c$antigen)) 
i = 0
res.stat.test = ""

for (a in antigens){

    print(a)
    df = dat_c %>% filter(antigen == a)
    stat.test = df %>%
    group_by(region) %>%
    wilcox_test(., norm_mean ~ genotype, alternative = "greater") %>%
    adjust_pvalue(method = "bonferroni") %>%
    add_significance("p.adj") %>%
    add_xy_position(x = "region", fun = "max", dodge = 0.8)

    if (i == 0){
    res.stat.test = stat.test
    } else {
    res.stat.test = rbind(res.stat.test, stat.test)
    }

}

plt_c <- ggplot(dat_c , aes(x = region , y = norm_mean , color = genotype)) + 
  geom_boxplot(outlier.shape=NA) +
  geom_jitter(position=position_jitterdodge()) +
  facet_wrap(~antigen , scales = "free" ) +
  stat_pvalue_manual(res.stat.test, label = "p.adj", tip.length = 0.05, step.increase = 0.01) + 
  ggtitle(label = "DRS hit IHC in tent5c KO")