Stat_compare_means within and between groups

Question

This is my first R attempt. I want to use stat_compare_means to compare means within subgroups as well as means from different subgroups. And I need the x-axis labeled by Treatment. I am aiming for some thing like this

My data looks like the following

    A tibble: 9 x 3
  Treatment Group     Count
  <chr>     <chr>     <dbl>
1   +         a        12
2   +         a        13
3   +         a        11
4   +         b        14
5   +         b        15
6   +         b        15
7   -         c        22
8   -         c        24
9   -         c        21 

I treid several attemps with ggbarplot and geom_bar but none worked. Is my plan even possible with stat_compare_means? Any help is appreciated.

My last try was this:

library(ggpubr)
library(ggplot2)
df <- structure(list(Treatment = c("+", "+", "+", "+", "+", "+", "-", "-", "-"), 
                 Group = c("a", "a", "a", "b", "b", "b", "c", "c", "c"), 
                 Count = c(12, 13, 11, 14, 15, 15, 22, 24, 21)), row.names = c(NA, -9), class = "data.frame")


ggbarplot(df, x = "Treatment", y = "Count", add = "mean_se", error.plot = "upper_errorbar",
      color = "Group",
      position = position_dodge(0.8))+

  stat_compare_means(df, comparisons = list(c("a","b" ), c("a","c"),c("b","c")),
                  label = "p.signif")  

Which returns in

Computation failed in `stat_signif()`:
Missing value, where TRUE/FALSE is needed

Answer 1

Try something like this:

library(ggpubr)
library(ggplot2)
#Comp
my_comparisons = list( c("+.a","+.b"),c("+.a","-.c"),c("+.b","-.c"))
#Plot
ggplot(df,aes(x=interaction(Treatment,Group),y=Count,fill=Group,group=Group))+
  geom_boxplot(position = position_dodge2(width = 0.5,preserve = 'single'))+
  theme_bw()+
  stat_compare_means(comparisons = my_comparisons,
                     method = 't.test')+
  theme(legend.position = 'top',
        panel.grid = element_blank(),
        axis.text = element_text(face='bold',color='black'),
        axis.title = element_text(face='bold',color='black'),
        strip.text = element_text(face='bold',color='black'),
        legend.text = element_text(face='bold',color='black'),
        legend.title = element_text(face='bold',color='black'),
        plot.title = element_text(face='bold',color='black',hjust=0.5))+
  ggtitle('My plot')

Output:

Some data used:

#Data
df <- structure(list(Treatment = c("+", "+", "+", "+", "+", "+", "-", 
"-", "-"), Group = c("a", "a", "a", "b", "b", "b", "c", "c", 
"c"), Count = c(12L, 13L, 11L, 14L, 15L, 15L, 22L, 24L, 21L)), row.names = c(NA, 
-9L), class = "data.frame")