rel_heights in plot_grid not responding

Question

I have two ggplots I'm trying to put together using cowplot's plot_grid:

First data.frame and ggplot:

require(ggplot2)
main.df <- data.frame(sample=c(paste("E.plus.A.plus",1:3,sep="_"),paste("E.minus.A.plus",1:3,sep="_"),paste("E.plus.A.minus",1:3,sep="_"),paste("E.minus.A.minus",1:3,sep="_")),
                      replicate=rep(1:3,4),cpm=c(rnorm(12)),
                      factor.level=factor(c(rep("E.plus.A.plus",3),rep("E.minus.A.plus",3),rep("E.plus.A.minus",3),rep("E.minus.A.minus",3)),
                                          levels=c("E.plus.A.plus","E.minus.A.plus","E.plus.A.minus","E.minus.A.minus")))

main.plot <- ggplot(main.df,aes(x=replicate,y=cpm,color=factor.level))+geom_point(size=3)+
  facet_wrap(~factor.level,ncol=length(levels(main.df$factor.level)))+
  labs(x="replicate",y="cpm")+scale_x_continuous(breaks=unique(main.df$replicate))+theme_bw()+
theme(legend.position="none",panel.border=element_blank(),strip.background=element_blank(),axis.title=element_text(size=8),plot.title=element_text(size=9,hjust=0.5))

Second data.frame and ggplot:

effects.df <- data.frame(factor.level=c("E.plus.A.plus-E.minus.A.plus","E.plus.A.plus-E.plus.A.minus","E.plus.A.plus-E.minus.A.minus",
                                        "E.minus.A.plus-E.plus.A.minus","E.minus.A.plus-E.minus.A.minus","E.plus.A.minus-E.minus.A.minus"),
                         effect=rnorm(6),effect.df=runif(6,0,0.5),p.value=runif(6,0,1),y=1:6+0.2)
effects.df$effect.high <- effects.df$effect+effects.df$effect.df
effects.df$effect.low <- effects.df$effect-effects.df$effect.df
effects.df$factor.level <- factor(effects.df$factor.level,levels=effects.df$factor.level)

sub.plot <- ggplot(effects.df,aes(x=effect,y=factor.level,color=factor.level))+geom_point(size=2.5,shape=19)+geom_errorbarh(aes(xmax=effect.high,xmin=effect.low),height=0.1)+
  geom_vline(xintercept=0,linetype="longdash",colour="black",size=0.25)+theme_bw()+theme(legend.position="none",panel.border=element_blank(),strip.background=element_blank(),axis.title=element_text(size=7),axis.text=element_text(size=7),legend.text=element_text(size=7),legend.title=element_text(size=7))+
  geom_text(aes(x=effects.df$effect,y=effects.df$y,label=format(signif(effects.df$p.value,2),scientific=T)),size=2.5)

My plot_grid command is:

require(cowplot)
plot_grid(main.plot,sub.plot,ncol=2,nrow=1,rel_widths=c(2,1.75),rel_heights=c(1,0.5))

as I want sub.plot to be half the height of main.plot and bottom aligned. This is what I'm getting though:

Playing around with rel_heights doesn't seem to change anything.

Answer 1

rel_heights allocates vertical space when you have two or more plots stacked one on top of the other. Since you have only one row of plots here, rel_heights doesn't do anything. For example, run plot_grid(main.plot, sub.plot, rel_heights=c(2,1), ncol=1) to see how rel_heights works.

To get the layout you want, you can stack an empty grob (graphics object) on top of the right-hand plot, which will result in the right-hand plot taking up half the vertical space available. In the code below, we use arrangeGrob from the gridExtra package to stack a nullGrob() on top of sub.plot. Then we place the output of arrangeGrob next to main.plot. By default, the two grobs arrangeGrob will each take up half the vertical space. However, if you decided, for example, that you want sub.plot to take up 2/3 of the vertical space, you would do arrangeGrob(nullGrob(), sub.plot, ncol=1, heights=c(1,2)).

require(cowplot)
require(gridExtra)
require(grid)

plot_grid(main.plot, arrangeGrob(nullGrob(), sub.plot, ncol=1), 
          ncol=2, rel_widths=c(2,1.75))