Hello Ghada ,

Ok, I revised my answer based on the error message you posted, below. I marked the areas where the main changes are like this: ########.

It's most likely the error is being generated when you call scale_y_log10() which could produce Inf or -Inf values. You can prevent that by restricting the input values to positive values only:

library(ggplot2)
library(dplyr)
library(ggpubr)
library(patchwork)

######## Begin by getting y_limits for both plots:
# Filter and prepare data for the first plot
a_filtered <- a %>%
  filter(name == "norm_CntTs", !is.na(coding), value > 0)  # Ensure only positive values for log scale

# Filter and prepare data for the second plot
a_filtered_tv <- a %>%
  filter(name == "norm_CntTv", !is.na(coding), value > 0)  # Ensure only positive values for log scale

# Combine the y-axis limits from both datasets
combined_data <- bind_rows(a_filtered, a_filtered_tv)
y_limits <- c(min(combined_data$value, na.rm = TRUE), max(combined_data$value, na.rm = TRUE))  # Define y-axis limits based on both datasets
########  now, can use y_limits in both plots below:

# Create the first plot with specified y-axis limits
plot1 <- ggplot(a_filtered, aes(x = Condition, y = value, color = Condition)) +
  geom_boxplot(width = 0.5, show.legend = FALSE) +
  scale_y_log10() +
  coord_cartesian(ylim = y_limits) +  # Apply consistent y-axis limits
  scale_size(range = c(0, 0.2))+
  scale_color_manual(values = c("HRSV" = "#eb4a40", "HRSV_RBV" = "#045275")) +
  facet_wrap(. ~ coding, ncol = 2) +
  labs(title = "Ts", y = "Average Ts count") +
  theme_bw() +
  theme(text = element_text(size = 19, face="bold"),
        plot.title = element_text(hjust = 0.5),
        strip.text = element_text(face = "bold"))

p1 <- plot1 + stat_compare_means(method = "wilcox.test", comparisons = my_comparisons, size= 4.5, hjust= 0.09, vjust=-0.2, alternative = "two.sided", paired = FALSE, label = "p.value")

# Create the second plot with the same y-axis limits
plot2 <- ggplot(a_filtered_tv , aes(x = Condition, y = value, color = Condition)) +
  geom_boxplot(width = 0.5, show.legend = FALSE) +
  scale_y_log10() +
  coord_cartesian(ylim = y_limits) +  # Apply consistent y-axis limits
  scale_size(range = c(0.01, 0.2))+
  scale_color_manual(values = c("HRSV" = "#eb4a40", "HRSV_RBV" = "#045275")) +
  facet_wrap(. ~ coding, ncol = 2) +
  labs(title = "Tv", y = "Average Tv count") +
  theme_bw() +
  theme(text = element_text(size = 19, face="bold"),
        plot.title = element_text(hjust = 0.5),
        strip.text = element_text(face = "bold"))

p2 <- plot2 + stat_compare_means(method = "wilcox.test", comparisons = my_comparisons, size= 4.5, hjust= 0.09, vjust=-0.2, alternative = "two.sided", paired = FALSE, label = "p.value")

# Combine the plots
combined_plot <- p1 + p2  # Combine the two plots using patchwork

# Display the combined plot
print(combined_plot)

Does this fix your error message? Let me know and we can keep trying.

VAL