Adding text for individual plots in ggplot facet_wrap

[bioinfguru]

Hi all,

I am adding 5 MA plots to facet_wrap, 1 for each tissue, showing the differential expression results from deseq2. For each plot, I want to add the total count of Up and Down regulated genes. It works perfectly well on an individual plot, but not when the plots are wrapped together. I am trying 3 options: geom_text, annotate, and scale_color_manual. However, no matter what I try, all numbers on the plot are from the same tissue (Ileum).

Thanks everyone in advance.
Kenneth

For a single tissue

Data structure/summary:

> head(res)
# A tibble: 6 × 3
  baseMean log2FoldChange signif
     <dbl>          <dbl> <fct> 
1   82014.          0.115 NS    
2     555.          0.328 NS    
3     119.          0.512 NS    
4     127.          0.115 NS    
5     232.         -0.230 NS    
6    1200.         -0.125 NS    
> summary(res$signif)
   Up  Down    NS 
  379   115 13831 

Create Plot for one tissue:

ggplot(data=res, aes(x = log2(baseMean), y = log2FoldChange, colour = signif))+ 
  geom_point(alpha = 1, size = 1, show.legend = TRUE) + 
  geom_hline(aes(yintercept = 0), colour = "black", linewidth = 0.5) +
  geom_hline(aes(yintercept = 0.58), colour = "black", linewidth = 0.5, linetype = "dashed") +  
  geom_hline(aes(yintercept = -1), colour = "black", linewidth = 0.5, linetype = "dashed") +  
  
  ######## TESTING #######
# option 1
geom_text(aes(x = 20, y = 5, label = paste("Up:", sum(signif=="Up"), "(with geom_text)", sep = "\t")), size = 3, color = colorspace::lighten("black", amount = 0.5)) +
  
  # option 2
  annotate(geom="text", x = 20, y = 4, label = paste("Up:", sum(res$signif=="Up"), "(with annotate)", sep = "\t"), size = 3) +
  
  # option 3
  scale_color_manual(values = c("darkred", "darkblue", "grey"),
                     labels = c(paste("Up", sum(res$signif=="Up"), sep = ": "),
                                paste("Down", sum(res$signif=="Down"), sep = ": "),
                                "Not Significant"),
                     drop = FALSE) +
  ########################
  labs(title = "Liver",
       color = "") +
  xlab("Log2 Mean expression") + 
  ylab("Log2 Fold Change") + 
  theme_bw()+
  theme(
    #legend.position = "inside",
    #legend.position.inside = c(0.9, 0.85),
    legend.position = "bottom",
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    strip.background = element_rect()
  )

For all tissues

Data structure/summary:

> head(res_signif)
# A tibble: 6 × 4
  baseMean log2FoldChange signif tissue  
     <dbl>          <dbl> <fct>  <chr>   
1   25297.         0.0696 NS     Duodenum
2     934.        -0.128  NS     Duodenum
3     286.         0.346  NS     Duodenum
4     573.         0.0357 NS     Duodenum
5    1242.         0.146  NS     Duodenum
6     117.        -0.185  NS     Duodenum
> counts
# A tibble: 5 × 4
  tissue      Up  Down    NS
  <chr>    <int> <int> <int>
1 Duodenum     2     1 15711
2 Ileum        0     0 16069
3 Jejunum     29    30 15830
4 Liver      379   115 13831
5 Muscle       5     0 13154

Create plot for all tissues with facet_wrap:

ggplot(data = res_signif, aes(x = log2(baseMean), y = log2FoldChange, colour = signif))+ 
  geom_point(alpha = 1, size = 1, show.legend = TRUE) + 
  geom_hline(aes(yintercept = 0), colour = "black", linewidth = 0.5) +
  geom_hline(aes(yintercept = 0.58), colour = "black", linewidth = 0.5, linetype = "dashed") +  
  geom_hline(aes(yintercept = -1), colour = "black", linewidth = 0.5, linetype = "dashed") +  
  ylim(-6, 6) + 
  labs(title = "RFI High v Low in T1",
       caption = "padj < 0.05, min fc +/- 0.5",
       color = "") +
  xlab("Log2 Mean expression") + 
  ylab("Log2 Fold Change") + 
  
  ######## TESTING #######
  # option 1
  geom_text(aes(x = 15, y = 5, label = paste(name, "Up:", pull(filter(counts, tissue == name), Up), "(with geom_text)", sep = "\t")), size = 3, color = colorspace::lighten("black", amount = 0.5)) +
  
  # option 2
  annotate(geom="text", x = 15, y = 4, label = paste(name, "Up:", pull(filter(counts, tissue == name), Up), "(with annotate)", sep = "\t"), size = 3) +
  
  # option 3
  scale_color_manual(values = c("darkred", "darkblue", "grey"),
                     labels = c(paste(name, "Up", pull(filter(counts, tissue == name), Up), sep = ": "),
                                paste(name, "Down", pull(filter(counts, tissue == name), Up), sep = ": "),
                                "Not Significant"),
                     drop = FALSE
  ) +
  ########################
  theme_bw()+
  theme(
    #legend.position = "inside",
    #legend.position.inside = c(0.9, 0.85),
    legend.position = "bottom",
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    strip.background = element_rect()
  ) + facet_wrap(vars(tissue))

[FJCC]

Here is a working example of putting different text in each facet. I think the key difference to your example is that I assign DF2 (the equivalent of your counts data frame) to the data argument of geom_text().

library(ggplot2)
#> Warning: package 'ggplot2' was built under R version 4.3.3
DF1 <- data.frame(X = rep(c(1,2), 4), Y = c(1,2, 1.1,2.1,1.2,2.2,1.3,2.3),
                  tissue = c("D","D","I","I","L","L","M","M"))
DF2 <- data.frame(tissue = c("D","I","L","M"), Lab = c("W","X","Y","Z"))

ggplot(DF1, aes(x = X, y = Y, group = tissue)) + geom_point() +
  geom_text(aes(x = 1.5, y = 1.5, label = Lab), data = DF2) +
  facet_wrap(~tissue)

^{Created on 2024-07-31 with reprex v2.0.2}

[bioinfguru]

Excellent, so simple (and frustrating). Thank you!