How to align multiple ggplot2 plots and add shadows over all of them

Question

Please download the data here!

Target: Plot an image like this:

Features: 1. two different time series; 2. the lower panel has a reverse y-axis; 3. shadows over two plots.

Possible solutions:
1. Facetting is not appropriate - (1) can not just make one facet's y axis reverse while keep the other(s) unchanges. (2) difficult to adjust the individual facets one by one.
2. Using viewports to arrange individual plots using the following codes:

library(ggplot2) library(grid) library(gridExtra)  ##Import data df<- read.csv("D:\\R\\SF_Question.csv")  ##Draw individual plots #the lower panel p1<- ggplot(df, aes(TIME1, VARIABLE1)) + geom_line() + scale_y_reverse() + labs(x="AGE") + scale_x_continuous(breaks = seq(1000,2000,200), limits = c(1000,2000)) #the upper panel p2<- ggplot(df, aes(TIME2, V2)) + geom_line() + labs(x=NULL) + scale_x_continuous(breaks = seq(1000,2000,200), limits = c(1000,2000)) + theme(axis.text.x=element_blank())  ##For the shadows #shadow position rects<- data.frame(x1=c(1100,1800),x2=c(1300,1850),y1=c(0,0),y2=c(100,100)) #make shadows clean (hide axis, ticks, labels, background and grids) xquiet <- scale_x_continuous("", breaks = NULL) yquiet <- scale_y_continuous("", breaks = NULL) bgquiet<- theme(panel.background = element_rect(fill = "transparent", colour = NA)) plotquiet<- theme(plot.background = element_rect(fill = "transparent", colour = NA)) quiet <- list(xquiet, yquiet, bgquiet, plotquiet) prects<- ggplot(rects,aes(xmin=x1,xmax=x2,ymin=y1,ymax=y2))+ geom_rect(alpha=0.1,fill="blue") + coord_cartesian(xlim = c(1000, 2000)) + quiet  ##Arrange plots pushViewport(viewport(layout = grid.layout(2, 1))) vplayout <- function(x, y)    viewport(layout.pos.row = x, layout.pos.col = y) #arrange time series print(p2, vp = vplayout(1, 1)) print(p1, vp = vplayout(2, 1)) #arrange shadows print(prects, vp=vplayout(1:2,1)) 

Problems:

1. the x-axis doesn't align correctly;
2. the shadow locations are wrong (because of the incorrect line-up of x-axis).

After Googling all around:

1. I firstly noticed that "align.plots() from ggExtra" could do this job. However, it has been deprecated by the author;
2. Then I've tried the gglayout solution, but no luck - I even could not install the "cutting-edge" package;

3. Finally, I've tried the gtable solution using the following code:

   gp1<- ggplot_gtable(ggplot_build(p1)) gp2<- ggplot_gtable(ggplot_build(p2)) gprects<- ggplot_gtable(ggplot_build(prects)) maxWidth = unit.pmax(gp1$widths[2:3], gp2$widths[2:3], gprects$widths[2:3]) gp1$widths[2:3] <- maxWidth gp2$widths[2:3] <- maxWidth gprects$widths[2:3] <- maxWidth grid.arrange(gp2, gp1, gprects) 

Now, the x-axis of upper and lower panel do align correctly. But the shadow positions are still wrong. And more importantly, I can not overlap the shadow plot on the two time-series. After several day's attempts, I nearly give up...

Could somebody here give me a hand?

Answer 1

You can achieve this particular plot also using just base plotting functions.

#Set alignment for tow plots. Extra zeros are needed to get space for axis at bottom. layout(matrix(c(0,1,2,0),ncol=1),heights=c(1,3,3,1))  #Set spaces around plot (0 for bottom and top) par(mar=c(0,5,0,5))  #1. plot plot(df$V2~df$TIME2,type="l",xlim=c(1000,2000),axes=F,ylab="")  #Two rectangles - y coordinates are larger to ensure that all space is taken   rect(1100,-15000,1300,15000,col="red",border="red") rect(1800,-15000,1850,15000,col="red",border="red")  #plot again the same line (to show line over rectangle) par(new=TRUE) plot(df$V2~df$TIME2,type="l",xlim=c(1000,2000),axes=F,ylab="")  #set axis axis(1,at=seq(800,2200,200),labels=NA) axis(4,at=seq(-15000,10000,5000),las=2)   #The same for plot 2. rev() in ylim= ensures reverse axis. plot(df$VARIABLE1~df$TIME1,type="l",ylim=rev(range(df$VARIABLE1)+c(-0.1,0.1)),xlim=c(1000,2000),axes=F,ylab="") rect(1100,-15000,1300,15000,col="red",border="red") rect(1800,-15000,1850,15000,col="red",border="red") par(new=TRUE) plot(df$VARIABLE1~df$TIME1,type="l",ylim=rev(range(df$VARIABLE1)+c(-0.1,0.1)),xlim=c(1000,2000),axes=F,ylab="") axis(1,at=seq(800,2200,200)) axis(2,at=seq(-6.4,-8.4,-0.4),las=2) 

UPDATE - Solution with ggplot2

First, make two new data frames that contain information for rectangles.

rect1<- data.frame (xmin=1100, xmax=1300, ymin=-Inf, ymax=Inf) rect2 <- data.frame (xmin=1800, xmax=1850, ymin=-Inf, ymax=Inf) 

Modified your original plot code - moved data and aes to inside geom_line(), then added two geom_rect() calls. Most essential part is plot.margin= in theme(). For each plot I set one of margins to -1 line (upper for p1 and bottom for p2) - that will ensure that plot will join. All other margins should be the same. For p2 also removed axis ticks. Then put both plots together.

library(ggplot2) library(grid) library(gridExtra) p1<- ggplot() + geom_line(data=df, aes(TIME1, VARIABLE1)) +    scale_y_reverse() +    labs(x="AGE") +    scale_x_continuous(breaks = seq(1000,2000,200), limits = c(1000,2000)) +     geom_rect(data=rect1,aes(xmin=xmin,xmax=xmax,ymin=ymin,ymax=ymax),alpha=0.1,fill="blue")+    geom_rect(data=rect2,aes(xmin=xmin,xmax=xmax,ymin=ymin,ymax=ymax),alpha=0.1,fill="blue")+    theme(plot.margin = unit(c(-1,0.5,0.5,0.5), "lines"))  p2<- ggplot() + geom_line(data=df, aes(TIME2, V2)) + labs(x=NULL) +    scale_x_continuous(breaks = seq(1000,2000,200), limits = c(1000,2000)) +    scale_y_continuous(limits=c(-14000,10000))+   geom_rect(data=rect1,aes(xmin=xmin,xmax=xmax,ymin=ymin,ymax=ymax),alpha=0.1,fill="blue")+   geom_rect(data=rect2,aes(xmin=xmin,xmax=xmax,ymin=ymin,ymax=ymax),alpha=0.1,fill="blue")+   theme(axis.text.x=element_blank(),         axis.title.x=element_blank(),         plot.title=element_blank(),         axis.ticks.x=element_blank(),         plot.margin = unit(c(0.5,0.5,-1,0.5), "lines"))   gp1<- ggplot_gtable(ggplot_build(p1)) gp2<- ggplot_gtable(ggplot_build(p2)) maxWidth = unit.pmax(gp1$widths[2:3], gp2$widths[2:3]) gp1$widths[2:3] <- maxWidth gp2$widths[2:3] <- maxWidth grid.arrange(gp2, gp1)