plot_grid function removes axis breaks from ggbreak in plots

Question

I'm struggling with a problem: I created two volcano plots in ggplot2, but due to the fact that I had one outlier point in both plot, I need to add y axis break for better visualization. The problem arises when I WANT TO plot both in the same page using plot_grid from cowplot::, because it visualizes the original plot without the breaks that I set.

 p<- c1 %>%
     ggplot(aes(x = avg_log2FC,
                y = -log10(p_val_adj),
                fill = gene_type,    
                size = gene_type,
                alpha = gene_type)) + 
     geom_point(shape = 21, # Specify shape and colour as fixed local parameters    
                colour = "black") + 
     geom_hline(yintercept = 0,
                linetype = "dashed") + 
     scale_fill_manual(values = cols) + 
     scale_size_manual(values = sizes) + 
     scale_alpha_manual(values = alphas) + 
     scale_x_continuous(limits=c(-1.5,1.5), breaks=seq(-1.5,1.5,0.5))  +
     scale_y_continuous(limits=c(0,110),breaks=seq(0,110,25))+
     labs(title = "Gene expression",
          x = "log2(fold change)",
          y = "-log10(adjusted P-value)",
          colour = "Expression \nchange") +
     theme_bw() + # Select theme with a white background  
     theme(panel.border = element_rect(colour = "black", fill = NA, size= 0.5),    
           panel.grid.minor = element_blank(),
           panel.grid.major = element_blank()) 
   p1 <- p + scale_y_break(breaks = c(30, 100))
   p1

p plot without breaks:

and p1 plot with breaks:

The same I did for the second plot. But this is the result using plot_grid(p1,p3, ncol = 2)

Can you help me understanding if I'm doing something wrong? or it is just a limitation of the package?

Answer 1

OP, it seems in that ggbreak is not compatible with functions that arrange multiple plots, as indicated in the documentation for the package here. There does seem to be a workaround via either print() (I didn't get this to work) or aplot::plot_list(...), which did work for me. Here's an example using built-in datasets.

# setting up the plots
library(ggplot2)
library(ggbreak)
library(cowplot)

p1 <-
ggplot(mtcars, aes(x=mpg, disp)) + geom_point() +
  scale_y_break(c(200, 220))

p2 <-
  ggplot(iris, aes(x=Sepal.Length, y=Sepal.Width, color=Species)) +
  geom_point() + scale_y_break(c(3.5, 3.7))

Plots p1 and p2 yield breaks in the y axis like you would expect, but plot_grid(p1,p2) results in the plots placed side-by-side without the y axis breaks.

The following does work to arrange the plots without disturbing the y axis breaks:

aplot::plot_list(p1,p2)