R - Secondary y-axis line not showing up when using gtable_add_grob

Question

I'm trying to overlay precipitation data over water quality data I've been collecting. I've made the water quality data and precipitation plots separately and am now trying to combine them using gtable_add_grob (a la http://rpubs.com/kohske/dual_axis_in_ggplot2). I've got the plot almost finished and looking good, but am running into a problem with the secondary y-axis not displaying. My code is as follows (for example):

y=(1:12)
y2=(12:1)
x=seq(as.Date("2014-01-01"), as.Date("2014-12-31"), by="months")
df=data.frame(x,y)
df2=data.frame(x,y2)

#plot1
g<-ggplot(df,aes(x,y))
g<-g+geom_bar(stat="identity",alpha=0.4)
g<-g+scale_y_reverse()
g<-g+theme(panel.grid = element_blank())
g<-g+theme(panel.background = element_blank())
g<-g+scale_x_date(labels = date_format("%b-%y"),breaks = date_breaks("months"))
g<-g+theme(axis.text.x = element_text(angle=45,hjust=1,color="black"))
g<-g+theme(axis.text.y = element_text(color="black"))
g<-g+theme(panel.grid = element_blank())
g<-g+theme(axis.line=element_line(colour="black"))
#print(g) #looks fine with axes lines

#plot2
g2<-ggplot(df,aes(x,y))
g2<-g2+geom_line()
g2<-g2+theme(panel.grid = element_blank())
g2<-g2+theme(panel.background = element_blank())
g2<-g2+scale_x_date(labels = date_format("%b-%y"),breaks = date_breaks("months"))
g2<-g2+theme(axis.text.x = element_text(angle=45,hjust=1,color="black"))
g2<-g2+theme(axis.text.y = element_text(color="black"))
g2<-g2+theme(panel.grid = element_blank())
g2<-g2+theme(axis.line=element_line(colour="black"))
#print(g2) #looks fine with axes lines

#combining them
gnew1<-ggplot_gtable(ggplot_build(g))
gnew2<-ggplot_gtable(ggplot_build(g2))
gg<-c(subset(gnew1$layout,name=="panel",se=t:r))
gnew<-gtable_add_grob(gnew2,gnew1$grobs[[which(gnew1$layout$name=="panel")]],pp$t,pp$l,pp$b,pp$l)
#attempted secondary axis    
ia<-which(gnew1$layout$name=="axis-l")
ga<-gnew1$grobs[[ia]]
ax<-ga$children[[2]]
ax$widths<-rev(ax$widths)
ax$grobs<-rev(ax$grobs)
ax$grobs[[1]]$x<-ax$grobs[[1]]$x - unit(1,"npc") + unit(0.15, "cm")
gnew<-gtable_add_cols(gnew,p1$widths[p1$layout[ia, ]$l], length(g1$widths) - 1)
gnew<-gtable_add_grob(gnew, ax, pp$t,length(gnew$widths)-1)
grid.draw(gnew)

This gives me a plot that looks like so:

My problem is that I want the secondary y-axis line to show up as well - you can see it's missing here. My original suspicion was that it had something to do with my making the panels grids and backgrounds blank for both graphs, but the axes lines on the independent graphs plot fine after use of

axis.line=element_line(colour="black")

Additionally, I need the clear backgrounds for the way this data will be displayed (so if it is this, is there a work around?). I went through the combining graphs portion of the code step by step and it seems to be working as intended. My output for the combined graph is

> gnew
TableGrob (6 x 6) "layout": 10 grobs
   z     cells       name                                 grob
1  0 (1-6,1-6) background      rect[plot.background.rect.1102]
2  3 (3-3,3-3)     axis-l absoluteGrob[GRID.absoluteGrob.1094]
3  1 (4-4,3-3)     spacer                       zeroGrob[NULL]
4  2 (3-3,4-4)      panel               gTree[GRID.gTree.1080]
5  4 (4-4,4-4)     axis-b absoluteGrob[GRID.absoluteGrob.1087]
6  5 (5-5,4-4)       xlab         text[axis.title.x.text.1096]
7  6 (3-3,2-2)       ylab         text[axis.title.y.text.1098]
8  7 (2-2,4-4)      title           text[plot.title.text.1100]
9  8 (3-3,4-4)     layout               gTree[GRID.gTree.1048]
10 9 (3-3,5-5)     layout                         gtable[axis]

This is similar to the output of the combined graph from my own data. Any thoughts on why the secondary y-axis line will not display?

Answer 1

So I found a work-around to the right y-axis when combining plots if anyone is looking at this later and is curious.

Using the gridExtra package, I created a manual border around the first plot's right side using borderGrob (see http://rgm3.lab.nig.ac.jp/RGM/R_rdfile?f=gridExtra/man/borderGrob.Rd&d=R_CC). The first plot may look a little "silly" when plotted on its own after applying the border, but my goal was to combine plots so the first independent plot doesn't really concern me. In addition I noticed a few mistypes in the example code where I didn't correct the copy and paste from the code I was using for my specific work, so sorry if anyone was trying to help and couldn't reproduce the example! The corrected code would go as follows:

##apologies for not adding these in the question 
library(ggplot2)
library(scales)
library(gtable)
library(gridExtra)

y=(1:12)
y2=(12:1)
x=seq(as.Date("2014-01-01"), as.Date("2014-12-31"), by="months")
df=data.frame(x,y)
df2=data.frame(x,y2)

#plot1
g<-ggplot(df,aes(x,y))
g<-g+geom_bar(stat="identity",alpha=0.4)
g<-g+scale_y_reverse()
g<-g+theme(panel.grid = element_blank())
g<-g+theme(panel.background = element_blank())
g<-g+scale_x_date(labels = date_format("%b-%y"),breaks = date_breaks("months"))
g<-g+theme(axis.text.x = element_text(angle=45,hjust=1,color="black"))
g<-g+theme(axis.text.y = element_text(color="black"))
##creating a border on the right side (type=3) ##make sure colour is spelled with a u!
gg<-borderGrob(type=3,colour="black",lwd=1)
##adding the new border
g<-g+annotation_custom(gg)
g<-g+theme(axis.line=element_line(colour="black"))
#print(g) ##now plotted with 3 axis lines (left, bottom, right)

#plot2
g2<-ggplot(df,aes(x,y))
g2<-g2+geom_line()
g2<-g2+theme(panel.grid = element_blank())
g2<-g2+theme(panel.background = element_blank())
g2<-g2+scale_x_date(labels = date_format("%b-%y"),breaks = date_breaks("months"))
g2<-g2+theme(axis.text.x = element_text(angle=45,hjust=1,color="black"))
g2<-g2+theme(axis.text.y = element_text(color="black"))
g2<-g2+theme(panel.grid = element_blank())
g2<-g2+theme(axis.line=element_line(colour="black"))
#print(g2) 

#combining them
gnew1<-ggplot_gtable(ggplot_build(g))
gnew2<-ggplot_gtable(ggplot_build(g2))
gg<-c(subset(gnew1$layout,name=="panel",se=t:r))
gnew<-gtable_add_grob(gnew2,gnew1$grobs[[which(gnew1$layout$name=="panel")]],gg$t,gg$l,gg$b,gg$l) ##fixed pp->gg
#extracting the axis from plot1  
ia<-which(gnew1$layout$name=="axis-l")
ga<-gnew1$grobs[[ia]]
ax<-ga$children[[2]]
ax$widths<-rev(ax$widths)
ax$grobs<-rev(ax$grobs)
ax$grobs[[1]]$x<-ax$grobs[[1]]$x - unit(1,"npc") + unit(0.15, "cm")
gnew<-gtable_add_cols(gnew,gnew1$widths[gnew1$layout[ia, ]$l], length(gnew2$widths) - 1) ##fixed g1->gnew ##fixed p1->gnew2 (twice)
gnew<-gtable_add_grob(gnew, ax, gg$t,length(gnew$widths)-1) ##fixed pp->gg
grid.draw(gnew)

This produces:

this!