Set the height of the graphs y-axis in grid.arrange, but not of the entire plot area

Question

When using grid arrange I encountered the following problem : I want all my panels (a,b,c) to have the same size, but as I have removed the labels and tickmarks from panel a and b (to have only a single x-axis) the size of the graphs a and b is bigger and equals the size of graph c + space for the lable and tick-marks of c. I cannot make use of ggplot2::facet_grid either, since I want to specify the y-axis limits independently (eg. of a until 40 and of b and c until 15). Below you can find the working example used to generate this plot, based upon this post to align the plots vertically, but I am clueless as how to assure the same height of each plot seperately. Any pointers are welcome.

library(ggplot2)
library(gridExtra)


# generate data  
data <- data.frame(values=c(runif(20,0,40),runif(40,0,15)),product=c(rep("a",20),rep("b",20),rep("c",20)),treat=c("e","f","g","h","i"),time=c(0,6,24,48))

my_labeller <- function(var, value){
  value <- as.character(value)
  value <- c("a","b","c")
  return(value)
}


#subset data
data_a <- data[1:20,]
data_b <- data[21:40,]
data_c <- data[41:60,]

# Make plots for all parameters seperatly:

p_a <- ggplot(data_a,fill = white,
                 aes(x=as.numeric(as.character(time)),y=as.numeric(as.character(values))))
p_a <- p_a+ geom_point(aes(colour=treat,shape=treat),size=4)
p_a <- p_a + geom_line(aes(colour=treat))
p_a <- p_a + theme(axis.ticks.x = element_line(colour = "grey"), 
                     axis.ticks.y =element_line(colour = "grey"),
                     panel.background = element_rect(fill = "white"),
                     panel.grid.major=element_blank(),
                     panel.grid.minor=element_blank(),
                     axis.line = element_line(colour = "grey"),
                     axis.text.x = element_text(size = 15),
                     axis.text.y = element_text(size = 15),
                     axis.title.x = element_text(size =18),
                     axis.title.y = element_text(size=18,angle=0),
                     legend.text = element_text(size=15),
                     legend.title = element_blank(),
                     legend.position = "right"

)

p_a <- p_a + scale_colour_manual(values = c("#FFFF55","#000000","#0000AA","#00AA00","#00AAAA"), breaks= c("e","f","g","h","i"), 
                                   labels = c("e","f","g","h","i")
) 
p_a <- p_a + scale_shape_manual(values =c(15:18,8), breaks= c("e","f","g","h","i"), 
                                labels = c("e","f","g","h","i") 
)

p_a <- p_a  + guides(color = guide_legend(nrow=5),size = 16)

# p <- p+ guides(colour="legend",size="none",shape= "legend")

p_a <- p_a + scale_x_continuous(breaks= c(0,6,24,48))
p_a <- p_a + xlab("Time (h)") + ylab(paste(data_a$product, "(mM)"))
p_a <- p_a + ylim(0,40)
print(p_a)



p_b <- ggplot(data_b,fill = white,
              aes(x=as.numeric(as.character(time)),y=as.numeric(as.character(values))))
p_b <- p_b+ geom_point(aes(colour=treat,shape=treat),size=4)
p_b <- p_b + geom_line(aes(colour=treat))
p_b <- p_b + theme(axis.ticks.x = element_line(colour = "grey"), 
                   axis.ticks.y =element_line(colour = "grey"),
                   panel.background = element_rect(fill = "white"),
                   panel.grid.major=element_blank(),
                   panel.grid.minor=element_blank(),
                   axis.line = element_line(colour = "grey"),
                   axis.text.x = element_text(size = 15),
                   axis.text.y = element_text(size = 15),
                   axis.title.x = element_text(size =18),
                   axis.title.y = element_text(size=18,angle=0),
                   legend.text = element_text(size=15),
                   legend.title = element_blank(),
                   legend.position = "right"

)

p_b <- p_b + scale_colour_manual(values = c("#FFFF55","#000000","#0000AA","#00AA00","#00AAAA"), breaks= c("e","f","g","h","i"), 
                                 labels = c("e","f","g","h","i")
) 
p_b <- p_b + scale_shape_manual(values =c(15:18,8), breaks= c("e","f","g","h","i"), 
                                labels = c("e","f","g","h","i") 
)

p_b <- p_b  + guides(color = guide_legend(nrow=5),size = 16)

# p <- p+ guides(colour="legend",size="none",shape= "legend")

p_b <- p_b + scale_x_continuous(breaks= c(0,6,24,48))
p_b <- p_b + xlab("Time (h)") + ylab(paste(data_b$product, "(mM)"))
p_b <- p_b + ylim (0,15)
print(p_b)




p_c <- ggplot(data_c,fill = white,
              aes(x=as.numeric(as.character(time)),y=as.numeric(as.character(values))))
p_c <- p_c+ geom_point(aes(colour=treat,shape=treat),size=4)
p_c <- p_c + geom_line(aes(colour=treat))
p_c <- p_c + theme(axis.ticks.x = element_line(colour = "grey"), 
                   axis.ticks.y =element_line(colour = "grey"),
                   panel.background = element_rect(fill = "white"),
                   panel.grid.major=element_blank(),
                   panel.grid.minor=element_blank(),
                   axis.line = element_line(colour = "grey"),
                   axis.text.x = element_text(size = 15),
                   axis.text.y = element_text(size = 15),
                   axis.title.x = element_text(size =18),
                   axis.title.y = element_text(size=18,angle=0),
                   legend.text = element_text(size=15),
                   legend.title = element_blank(),
                   legend.position = "right"

)

p_c <- p_c + scale_colour_manual(values = c("#FFFF55","#000000","#0000AA","#00AA00","#00AAAA"), breaks= c("e","f","g","h","i"), 
                                 labels = c("e","f","g","h","i")
) 
p_c <- p_c + scale_shape_manual(values =c(15:18,8), breaks= c("e","f","g","h","i"), 
                                labels = c("e","f","g","h","i") 
)

p_c <- p_c  + guides(color = guide_legend(nrow=5),size = 16)

# p <- p+ guides(colour="legend",size="none",shape= "legend")

p_c <- p_c + scale_x_continuous(breaks= c(0,6,24,48))
p_c <- p_c + xlab("Time (h)") + ylab(paste(data_c$product, "(mM)"))
p_c <- p_c + ylim (0,15)
print(p_c)

# now remove space in between a and b and b and c

p_a <- p_a + theme(plot.margin = rep(unit(0,"null"),4),
                     panel.margin = unit(0,"null"),
                     axis.ticks.length = unit(0,"null"),
                     axis.ticks.margin = unit(0,"null")) +
  labs(x=NULL) + 
  scale_x_discrete(breaks=NULL) + 
  guides(fill=FALSE)

p_b <- p_b + theme(plot.margin = rep(unit(0,"null"),4),
                         panel.margin = unit(0,"null"),
                         axis.ticks.length = unit(0,"null"),
                         axis.ticks.margin = unit(0,"null")) +
  labs(x=NULL) + 
  scale_x_discrete(breaks=NULL) + 
  guides(fill=FALSE)

p_c <- p_c + theme(plot.margin = rep(unit(0,"null"),4),
                           panel.margin = unit(0,"null"))

# arrange them (+ align) 

plots <- list(p_a,p_b,p_c)
grobs <- list()
widths <- list()


for (i in 1:length(plots)){
  grobs[[i]] <- ggplotGrob(plots[[i]])
  widths[[i]] <- grobs[[i]]$widths[2:5]
}

maxwidth <- do.call(grid::unit.pmax, widths)

for (i in 1:length(grobs)){
  grobs[[i]]$widths[2:5] <- as.list(maxwidth)
}


do.call("grid.arrange", c(grobs, ncol = 1))

I am using R on linux. The output of my session.Info() is:

R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C           
 [9] LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] gridExtra_0.9.1 ggvis_0.4       fastmatch_1.0-4 dplyr_0.3.0.2   shiny_0.10.2.1  xlsx_0.5.7      xlsxjars_0.6.1  rJava_0.9-6     ggplot2_1.0.0   reshape2_1.4    gdata_2.13.3   

loaded via a namespace (and not attached):
 [1] DBI_0.3.1        MASS_7.3-35      R6_2.0.1         RJSONIO_1.3-0    Rcpp_0.11.3      assertthat_0.1   colorspace_1.2-4 digest_0.6.4     gtable_0.1.2     gtools_3.4.1    
[11] htmltools_0.2.6  httpuv_1.3.2     labeling_0.3     magrittr_1.0.1   mime_0.2         munsell_0.4.2    parallel_3.1.1   plyr_1.8.1       proto_0.3-10     scales_0.2.4    
[21] stringr_0.6.2    tools_3.1.1      xtable_1.7-4

Ralli

Have you tried using ggplot2::facet_grid(scales="free_y") or do you need to manually specify different y limits rather than have them auto-generated? – Adigun

We do need to set the scales manually since if we use scales = free_y we get this sloppy result (see: bit.ly/1yyEd5C) where plot b and c have a different scale, whereas I would like them to range from 0-15 mM. – Ralli

Answer 1

You should use rbind instead of grid.arrange,

plots <- list(p_a, p_b, p_c)
grobs <- lapply(plots, ggplotGrob)
# for gridExtra < v2.3, use do.call(gridExtra::rbind.gtable, grobs)
# for gridExtra >= v2.3 use:
g <- do.call(gridExtra::gtable_rbind, grobs)

library(grid)
grid.newpage()
grid.draw(g)

Leyte

I get an error with this, "Error: 'rbind' is not an exported object from 'namespace:gridExtra'". I've installed the most recent version of gridExtra... am I missing something? – Vocalic

Answer 2

One hack could be to use facet_grid with scales = "free_y", and add some "invisible" data that will be used when ggplot automatically generates the y axis limits. This would work if you want to expand the automatically generated axes beyond the limits of your data, but not if you want to constrain them to exclude a portion of your data:

data <- data.frame(values=c(runif(20,0,40),runif(40,0,15)),
           product=c(rep("a",20),rep("b",20),rep("c",20)),
           treat=c("e","f","g","h","i"),
           time=c(0,6,24,48))

ggplot(data, aes(time, values, color=treat)) + 
      geom_line() + geom_point() +
      geom_hline(data=data.frame(product=c("a", "b", "c"), values=c(40, 15, 15)), 
             aes(yintercept=values), color="white") +
      facet_grid(product~., scales="free") +
      theme(panel.background=element_blank(), panel.grid=element_blank())

Adigun