Avoid multiple plots overlay in `pdf` function when looping

Question

I have to create some graphs through a loop. The graphs are multipaneled and each panel has three different layers. I tried this code

pdf('plot.pdf', width=14, height=7)

R <- dim(dataset)[1]

for (i in 1:R) {

  par(mfrow=c(1,2))

  par(mfg=c(1,1))
  plot(...)
  points(...)
  polygon(...)

  par(mfg=c(1,2)
  plot(...)
  points(...)
  polygon(....)

}

dev.off()

but the result is a single graph (and not one graph per loop) fully overlaid.

Graph

Is there an issue in looping with the par function?

EDIT: here's a reproducible example. I tried with split.screen, but the result is the same single-paged pdf with overlaid plots. The issue seems related to the pdf function itself, since the loop does the job correctly.

set.seed(123)

## create data
varA1 <- matrix(rnorm(60,5,1), nrow=3)
varA2 <- matrix(rnorm(60,5,1), nrow=3)
varB1 <- matrix(rnorm(80,20,10), nrow=4)
varB2 <- matrix(rnorm(80,30,20), nrow=4)
sitesA <- 1:nrow(varA1)
sitesB <- 1:nrow(varB1)
totsites <- 1:max(sitesA, sitesB)

## create pdf
pdf('prova.pdf', width=14, height=7)

for(i in totsites) { # the pdf should contain "totsites" number of pages (in this case, 4)
 split.screen(c(1,2))
 if(i %in% sitesA) { 
   screen(1)
   plot(var1[i,], ylim=c(0, max(c(var1, var2))), col='darkred', type='b', pch=16)
   points(var2[i,], col='red', type='b', pch=16)
   polygon(c(1:20,rev(1:20)),c(var1[i,]-1,rev(var1[i,]+1)), col=rgb(100, 0, 0, maxColorValue=255, alpha=50), border=NA)
 }
 if(i %in% sitesB) { 
   screen(2)
   plot(var3[i,], ylim=c(0, max(c(var3, var4))), col='darkgreen', type='b', pch=16)
   points(var4[i,], col='green', type='b', pch=16)
   polygon(c(1:20,rev(1:20)),c(var3[i,]-10,rev(var3[i,]+10)), col=rgb(0, 100, 0, maxColorValue=255, alpha=50), border=NA)
  }
}
dev.off()

BTW, I got this warning

Warning message:
In par(new = TRUE) : calling par(new=TRUE) with no plot

You should really provide a minimal [reproducible example](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). It's unclear exactly what you are doing in the `...` in your code. You are expecting one PDF with `R` different pages? — MrFlick, Feb 27 '17 at 21:38
Thank you @MrFlick, I edited the post with a reproducible example. Yes, I want a pdf with `R` different pages — Quechua, Mar 01 '17 at 12:43

score 0 · Accepted Answer · answered Mar 01 '17 at 16:12

Using layout() rather than split.screen() seems to be a better option. Also keep it outside the loop.

pdf('prova.pdf', width=14, height=7)
layout(matrix(1:2, nrow=1))
for(i in totsites) { # the pdf should contain "totsites" number of pages (in this case, 4)

 if(i %in% sitesA) { 
   plot(varA1[i,], ylim=c(0, max(c(varA1, varA2))), col='darkred', type='b', pch=16)
   points(varA2[i,], col='red', type='b', pch=16)
   polygon(c(1:20,rev(1:20)),c(varA1[i,]-1,rev(varA1[i,]+1)), col=rgb(100, 0, 0, maxColorValue=255, alpha=50), border=NA)
 } else {
   plot.new()
 }
 if(i %in% sitesB) { 
   plot(varB1[i,], ylim=c(0, max(c(varB1, varB2))), col='darkgreen', type='b', pch=16)
   points(varB2[i,], col='green', type='b', pch=16)
   polygon(c(1:20,rev(1:20)),c(varB1[i,]-10,rev(varB1[i,]+10)), col=rgb(0, 100, 0, maxColorValue=255, alpha=50), border=NA)
  } else {
   plot.new()
  }
}
dev.off()

Avoid multiple plots overlay in `pdf` function when looping

1 Answers1