scale_y_continuous() cause plotting issue

Question

There is strange issue using scale_y_continuous() and trying to plot text after that. e.g. if we remove scale_y_continuous() from below code then it is working fine but if we add scale_y_continuous() to limit y-axis then it is not displaying p-value content.

library(ggplot2)
library(ggpubr)

# Sample data
data <- data.frame(
  group = rep(c("A", "B"), each = 20),
  value = c(rnorm(20, mean = 50, sd = 10),
            rnorm(20, mean = 60, sd = 15))
)

# Create a boxplot with customized y-axis limits
p <- ggplot(data, aes(x = group, y = value)) +
  geom_boxplot() +
  scale_y_continuous(limits = c(30, 80))  # Adjust the y-axis visible range

# Add p-values using stat_compare_means()
p <- p +
  stat_compare_means(comparisons = list(c("A", "B")), label = "p.format")


# Display the plot
print(p)

Answer 1

Setting limits with scale_y_continuous removes data outside the limits. Instead we can zoom in with coord_cartesian. In the same function we can turn off clipping, and then update the theme to expand the plot's upper margin:

library(ggplot2)
library(ggpubr)


ggplot(data, aes(x = group, y = value)) +
  geom_boxplot() +
  coord_cartesian(ylim = c(30, 80),
                  clip = 'off') +
  stat_compare_means(comparisons = list(c("A", "B")), label = "p.format") +
  theme(plot.margin = unit(c(3,0,0,0), 'cm'))

^{Created on 2023-08-23 with reprex v2.0.2}