Tukey annotations on facet ggplot-CodePudding

I am trying to get annotations from a Tukey's test on to a facet'ed ggplot. I've tried multiple other answers (

I can get the confidence interval plots one gene at a time using:

test_stats_Tukey <- Raw_data %>%
  nest_by(Gene) %>%
  mutate(Model = list(glm(FC ~ Treatment * Age, data = data)))

par(mar=c(5,13,4,1) .1)
plot(TukeyHSD(x= aov(test_stats_Tukey[[3]][[1]]), conf.level=0.95) , las=1 , col="brown")

Which gives:

But I'd like to extract and plot annotations in facets automatically.

Any help would be great. Thank you!

CodePudding user response：

It's not pretty, but it gets the job done!

Final_ann <- data.frame()
for (ann_facet in as.character(unique(Raw_data$Gene))) {
  temp_ann_data <- Raw_data[which(Raw_data$Gene == ann_facet),]
  temp_ann_model <- glm(FC ~ Treatment * Age, 
               data = temp_ann_data)
  
  temp_ann_pairs <- emmeans(temp_ann_model, 
                                 pairwise ~ Treatment*Age, 
                                 adjust = "tukey")
  
  temp_ann_model_cld <- cld(temp_ann_pairs$emmeans, 
                                 alpha = .05,
                                 Letters = letters)
  
  temp_ann_letters <- arrange(temp_ann_model_cld, Age, Treatment)
  colnames(temp_ann_letters)[8] <- "Annotation"
  temp_ann_letters$Annotation <- gsub("[[:space:]]", "",as.character(temp_ann_letters$Annotation))
  temp_ann_letters$Gene <- ann_facet
  temp_ann_letters$FC <-1.25*max(temp_ann_data$FC)
  Final_ann <- rbind(Final_ann, temp_ann_letters[,c(1,2,8,9,10)])
}

Test_plot   
  geom_text(data = Final_ann,  
            aes(x = Age, y = log2(FC), group = Treatment, label=Annotation), 
            size=3, position = position_dodge(width = 0.75))  
  facet_wrap(Gene ~ ., ncol = 4, scales = "free")

CodePudding user response：

Please check out