[FIXED] Why is the wilcox.test results overlapping when I try to plot a graph?

Issue

I'm trying to get statistics on my faceted graph, but the output of the wilcoxon test are overlapped like this:

The code I am using is this:

ggplot(df, aes(y = count, x = time, group = time)) + 
  theme_bw() +
  geom_boxplot()+
  theme(legend.position = "none")+
  scale_y_log10(limits = c(1, 250)) +
  facet_wrap(vars(cluster), scales = "fixed")+
  stat_compare_means(method= "wilcox.test")
 labs(y = "Clone count", x = "Time point")

And my data looks like this:

structure(list(time = c("Day 0", "Day 0", "Day 0", "Day 0", "Day 0", 
"Day 0", "Day 0", "Day 0", "Day 0", "Day 0", "Day 1", "Day 1", 
"Day 1", "Day 1", "Day 1", "Day 1", "Day 1", "Day 1", "Day 1", 
"Day 1", "Day 2", "Day 2", "Day 2", "Day 2", "Day 2", "Day 2", 
"Day 2", "Day 2", "Day 2", "Day 2", "Day 2", "Day 2", "Day 2", 
"Day 2", "Day 2", "Day 2", "Day 2", "Day 2", "Day 2", "Day 2", 
"Day 2", "Day 2", "Day 2", "Day 2", "Day 2"), count = c(1L, 4L, 
1L, 1L, 1L, 1L, 2L, 3L, 1L, 1L, 59L, 1L, 1L, 1L, 3L, 1L, 2L, 
5L, 3L, 1L, 1L, 2L, 1L, 1L, 1L, 54L, 3L, 6L, 1L, 1L, 1L, 2L, 
1L, 1L, 7L, 1L, 3L, 1L, 207L, 5L, 3L, 3L, 11L, 2L, 1L), cluster = c("C", 
"C", "C", "C", "D", "D", "D", "D", "D", "D", "A", "A", "D", "D", 
"D", "C", "C", "C", "C", "C", "D", "D", "D", "D", "D", "B", "C", 
"B", "B", "C", "C", "C", "C", "C", "B", "B", "B", "A", "A", "A", 
"A", "A", "A", "A", "A")), row.names = c(NA, -45L), class = "data.frame")

Also, how would I add significance bars to this?

Solution

It may helps by specifying comparisons.

my_comparisons <- list(c("Day 0", "Day 1"), c("Day 1", "Day 2"), c("Day 0", "Day 2"))
ggplot(df1, aes(y = count, x = time)) + 
  theme_bw() +
  geom_boxplot()+
  theme(legend.position = "none")+
  scale_y_log10() +
  stat_compare_means(method= "wilcox.test", comparisons = my_comparisons)  +
  facet_wrap(.~(cluster), scales = "fixed")+
  labs(y = "Clone count", x = "Time point") +
  ylim(c(0,400))

Answered By - Park

Answer Checked By - Dawn Plyler (PHPFixing Volunteer)