Similar question How to align multiple ggplot2 plots and add shadows over all of them
I have spend several days on the above question, with no success.
Question
I want to add a vertical line on my plot. How to do that?
Data
Can downloaded here or minidata like following
CHROM BIN_START BIN_END N_VARIANTS cashmere_PI noncashmere_PI Fst log2ratio log10ratio ratio chr1 1 100000 83 0.000119082 0.000216189 0.0532838 0.860337761418733 0.25898747258944 1.81546329420064 chr1 50001 150000 72 9.67484e-05 0.00018054 0.0508251 0.90000880485528 0.27092964662313 1.86607737182217 chr1 100001 200000 56 7.98726e-05 0.000142246 0.0299909 0.832615502149238 0.250642241001749 1.78091110092823 chr1 150001 250000 62 8.53008e-05 0.00015624 0.0303362 0.873132677193208 0.262839126029552 1.831635811153 chr1 200001 300000 57 7.74641e-05 0.000133271 0.0405702 0.782763114550565 0.235635176979081 1.72042275066773 chr1 250001 350000 115 0.00015489 0.000186053 0.0662349 0.264469649364419 0.0796132974014257 1.20119439602298 chr1 300001 400000 118 0.00016185 0.000198862 0.0744181 0.29711025627991 0.0894390991596656 1.22868087735558 chr1 350001 450000 92 0.000125799 0.000228875 0.0581435 0.863439432015068 0.259921168475606 1.81937058323198 chr1 400001 500000 83 0.000110109 0.0002136 0.0561351 0.955979251468278 0.287778429924352 1.93989592131433 chr1 450001 550000 57 8.55834e-05 0.000148245 0.0909248 0.792580546810178 0.238590518569624 1.73217002362608 Code
pitab <- dget(file="dput") library(ggplot2) library(gtable) library(gridExtra) library(grid) pitab <- pitab[pitab$Fst>0 & pitab$ratio > 0 , ] dst <- density(pitab$Fst) Fst.dst <- data.frame(Fst = dst$x, density = dst$y) dens.pi <- density(pitab$log2ratio) q975 <- quantile(pitab$log2ratio,0.975) q025 <- quantile(pitab$log2ratio,0.025) dd.pi <- with(dens.pi,data.frame(x,y)) dd.pi <- dd.pi[dd.pi$x>0 ,] ### top plot top <- qplot(x,y,data=dd.pi, geom = "line") + geom_ribbon(data=subset(dd.pi,x>q975), aes(ymax=y,xmax=max(pitab$log2ratio),xmin=0, ymin=0), fill="green", alpha=0.5)+ geom_ribbon(data=subset(dd.pi,x<q025), aes(ymax=y,xmax=max(pitab$log2ratio),xmin=0, ymin=0), fill="blue", alpha=0.5 ) + geom_ribbon(data=subset(dd.pi,x>q025 & x<q975), aes(ymax=y,xmax=max(pitab$log2),xmin=0, ymin=0), fill="grey", alpha=0.5) + geom_hline(yintercept=0,col="black",lwd=0.5) + labs(x="log2ratio",y="density") ### empty plot on top right empty <- ggplot()+geom_point(aes(1,1), colour="white")+ theme(axis.ticks=element_blank(), panel.background=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.title.x=element_blank(), axis.title.y=element_blank()) ### scatter plot bottom left q95 <- quantile(pitab$Fst, .95) dd <- with(pitab,data.frame(Fst,log2ratio)) scatter <- ggplot(dd,aes(x=log2ratio,y=Fst)) + geom_point(data=subset(dd, Fst > q95 & log2ratio < q025), aes(x=log2ratio,y=Fst,ymin=0,ymax=Fst,xmin=0,xmax=max(pitab$log2ratio)),colour="purple",alpha=0.8) + geom_point(data=subset(dd, Fst > q95 & log2ratio > q975), aes(x=log2ratio,y=Fst,ymin=0,ymax=Fst,xmax=max(pitab$log2ratio),xmin=0),colour="yellow", alpha = 0.8) + geom_point(data=subset(dd, !((Fst > q95 & log2ratio > q975) | (Fst > q95 & log2ratio < q025) ) ), aes(x=log2ratio,y=Fst,ymin=0,ymax=Fst,xmax=max(pitab$log2ratio),xmin=0),colour="black", alpha = 0.4) ## right plot ## dens.f <- density(pitab$Fst) q75 <- quantile(pitab$Fst, .75) q95 <- quantile(pitab$Fst, .95) dd.f <- with(dens.f,data.frame(x,y)) dd.f <- dd.f[dd.f$x > 0 ,] #library(ggplot2) right <- qplot(x,y,data=dd.f,geom="line")+ geom_ribbon(data=subset(dd.f,x>q95),aes(ymax=y),ymin=0,fill="red",colour=NA,alpha=0.5) + geom_ribbon(data=subset(dd.f,x<q95),aes(ymax=y),ymin=0, fill="grey",colour=NA,alpha=0.5) + geom_hline(yintercept=0,col="black",lwd=0.5) + coord_flip() #### the vline i want to add line <- ggplot()+geom_vline(aes(1,1), xintercept = q025) g.top <- ggplotGrob(top) g.scatter <- ggplotGrob(scatter) g.empty <- ggplotGrob(empty) g.right <- ggplotGrob(right) g.line <- ggplotGrob(line) tab <- gtable(unit(rep(1, 3), "null"), unit(rep(1, 3), "null")) tab <- gtable_add_grob(tab, g.top, t = 1, l = 1, r = 2) tab <- gtable_add_grob(tab, g.scatter, t = 2 , l = 1, r=2,b=3) tab <- gtable_add_grob(tab, g.empty,t=1,r=3,l=3) tab <- gtable_add_grob(tab,g.right, r=3,t=2,b=3,l=3) #tab <- gtable_add_grob(tab,g.line, r=2,t=1,b=3,l=1) plot(tab) I get following picture:
looks good!
But, when I release the code:
tab <- gtable_add_grob(tab,g.line, r=2,t=1,b=3,l=1) I only get one vertical line, top plot and scatter plot have been overwrited.
I also try to imitate the Claus Wilke's solution, using following code :
g.top <- ggplotGrob(top) index <- subset(g.top$layout, name == "axis-b") names <- g.top$layout$name[g.top$layout$t<=index$t] g.top <- gtable_filter(g.top, paste(names, sep="", collapse="|")) # set height of remaining, empty rows to 0 for (i in (index$t+1):length(g.top$heights)) { g.top$heights[[i]] <- unit(0, "cm") } # Table g1 will be the bottom table. We chop off everything above the panel g.scatter <- ggplotGrob(scatter) index <- subset(g.scatter$layout, name == "panel") # need to work with b here instead of t, to prevent deletion of background names <- g.scatter$layout$name[g.scatter$layout$b>=index$b] g.scatter <- gtable_filter(g.scatter, paste(names, sep="", collapse="|")) # set height of remaining, empty rows to 0 for (i in 1:(index$b-1)) { g.scatter$heights[[i]] <- unit(0, "cm") } # bind the two plots together g.main <- rbind(g.top, g.scatter, size='first') #grid.newpage() #grid.draw(g.main) # add the grob that holds the shadows g.line <- gtable_filter(ggplotGrob(line), "panel") # extract the plot panel containing the shadows index <- subset(g.main$layout, name == "panel") # locate where we want to insert the shadows # find the extent of the two panels t <- min(index$t) b <- max(index$b) l <- min(index$l) r <- max(index$r) # add grob g.main <- gtable_add_grob(g.main, g.line, t, l, b, r) # plot is completed, show grid.newpage() grid.draw(g.main) But I only get a vertical line.
