Change the number of decimals in stat_compare_means

I know there are some questions similar to this but I have tried the suggested answer and I was not able to figure out how to change the number of decimals in stat_compare_means Maybe it is because I am not comparing all the values against each other but only some of them.

my code is:

library(tidyverse)
library(ggbeeswarm)
library(ggpubr)

set.seed(123) 

data <- data.frame(
 plot = rep(c("cl", "ct", 
              "rt", "rl"), each = 10),
 value = c(rnorm(10, mean = 3.5, sd = 0.3),   # Control lower canopy
          rnorm(10, mean = 3.7, sd = 0.3),   # Control upper canopy
          rnorm(10, mean = 4.0, sd = 0.3),   # Released upper canopy
          rnorm(10, mean = 4.2, sd = 0.3))   # Released lower canopy
)

summary_data <- data %>%
 group_by(plot) %>%
 summarise(
  value_Mean = mean(value),
  value_SE = sd(value) / sqrt(n())
 )

comparisons <- list(
 c("cl", "ct"),
 c("ct", "rt"),
 c("rt", "rl"),
 c("cl", "rl")
)

ggplot(data, aes(x = plot, y = value)) +
 geom_beeswarm(aes(color = plot),size = 5, alpha = 0.6) +
 geom_errorbar(
  data = summary_data, 
  aes(y = value_Mean, ymin = value_Mean - value_SE, ymax = value_Mean + value_SE),
  width = 0.2, size = 0.8, color = "black"
 ) +
 geom_point(
  data = summary_data, 
  aes(y = value_Mean), color = "red", size = 8
 ) +
 stat_compare_means(
  comparisons = comparisons, method = "t.test", label = "p.format", 
  label.y = c(4.3, 4.8, 5.3, 5.8), 
  size = 10
 )

I tried adding decimal=3 in the label, or add format.pval = function(p) format(p, digits = 3) I either get no difference or an error appears.

What am I doing wrong? If you could point me to the question that can answer this problem I will highly appreciate it

BR

The canonical solution in ggsignif::geom_signif -- for which ggpubr::stat_compare_means is mostly a wrapper -- is to use the map_signif_level= argument that can take an arbitrary function to format the P-values.

Unfortunately, that argument is hijacked by ggpubr in a way that only tries to guess whether you want to replace the values by stars using the non-exported .is_p.signif_in_mapping().

A much easier solution is to use just a direct geom_signif, with the two caveats that it takes test= and y_position= rather than method= and label.y= arguments (with the exact same meaning):

## Replace only the very last ggpubr::stat_compare_means call
... +
 ggsignif::geom_signif(
  comparisons = comparisons, test = "t.test", 
  y_position = c(4.3, 4.8, 5.3, 5.8), 
  size = 1, map_signif_level = \(p) sprintf("%.3f", p)
 )