Good morning everyone, I have this issue while using ggplot and creating a bar chart with two axes. I've managed to get the bars as I wanted, but I can't seem to change the axis labels on the x-axis. Every two bars correspond to "Resistant" and "Susceptible." Then, the first 12 bars are for 48 hpi, and the last 4 are for 72 hpi. Lastly, the first 4 columns are for "Blood," the next 4 for "Lung," and the last 8 correspond to "Nasal Turbinate." I would like to label these on the x-axis, but I can't figure it out."

 DF_blood <- data.frame(Group = c("Resistant", "Susceptible"), 
                  Host_DEGs = c(3558, 5635), 
                  Viral_counts = c(0.4771213, 5.608774))

 DF_Lung <- data.frame(Group = c("Resistant", "Susceptible"), 
                  Host_DEGs = c(126, 10866), 
                  Viral_counts = c( 1.531479, 6.325484))


 DF_NasalT_72 <- data.frame(Group = c("Resistant", "Susceptible"), 
                  Host_DEGs = c(2830, 4632), 
                  Viral_counts = c(0, 4.716613))

 DF_NasalT_48 <- data.frame(Group = c("Resistant", "Susceptible"), 
                  Host_DEGs = c(81, 6126), 
                  Viral_counts = c(2.41162, 4.985206))


 # Combina los dataframes DF de sangre, pulmón y turbinate nasal en uno solo
 combined_df <- rbind(DF_blood, DF_Lung, DF_NasalT_48, DF_NasalT_72)


 DFlong <-  combined_df |> pivot_longer(cols = -Group, names_to = "Type") |> 
   mutate(scaled_value = ifelse(Type == "Host_DEGs", value, value / 0.001))



 combined_df$Sample <- c("Blood", "Blood", "Blood", "Blood", "Lung", "Lung", "Lung", "Lung", "Nasal_Turbinate","Nasal_Turbinate", "Nasal_Turbinate","Nasal_Turbinate", "Nasal_Turbinate", "Nasal_Turbinate","Nasal_Turbinate")

 combined_df$Timepoint <- c("48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","72hpi","72hpi")


 DFlong <- DF |> pivot_longer(cols = -Group, names_to = "Type") |> 
   mutate(scaled_value = ifelse(Type == "Host_DEGs", value, value / 0.001))

 DFlong$Sample <- c("Blood", "Blood", "Blood", "Blood", "Lung", "Lung", "Lung", "Lung", "Nasal_Turbinate", "Nasal_Turbinate", "Nasal_Turbinate", "Nasal_Turbinate", "Nasal_Turbinate", "Nasal_Turbinate", "Nasal_Turbinate","Nasal_Turbinate")

 DFlong$Timepoint <- c("48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","48hpi","72hpi","72hpi","72hpi","72hpi")


 ggplot(DFlong, aes(x = interaction(Group, Timepoint, Sample), y = scaled_value, fill = Type)) + 
   geom_col(position = "dodge") + 
   scale_y_continuous(name = "Host DEGs", limits = c(0, 11000), sec.axis = sec_axis(~ . * 0.0009, name = "Viral gene counts (log10)")) +
   labs(y = "Host DEGs") +
   theme_minimal() +
   theme(text = element_text(size = 20)) +
   coord_cartesian(ylim = c(0, 7500)) +
   annotate("text", x = 1:4, y = - 400,
            label = rep(c("Resistant", "Susceptible"), 2)) +
   annotate("text", c(1.5, 3.5), y = - 800, label = c("48 hpi", "48 hpi"))


sessionInfo( )

ggplot2 is not a Bioconductor package. You might try asking on either the tidyverse forum or maybe at biostars.org or stackoverflow.com.