combine multiple pdf plots into one file

I asked a similar question a while back and Ananda Mahto generously provide time and code to help make a github package that can combine multiple plots of different sizes. I use it in my workflow a bit but have no plans to push it to CRAN but you can download it with the devtools package. Note that you have to have ghostscript installed and on your path for this to work:

## Getting the plotflow github package:

library(devtools)
install_github("plotflow", "trinker")
library(plotflow)

## 2 Examples using the package to merge multiple pdfs

## Example 1
merge_pdf(3, file = "foo.pdf", widths = c(7, 7, 10), heights = c(6, 10, 7))
plot(1:10)
plot(1:10, pch=19)
plot(1:10, col="red", pch=19)

## Example 2
library(ggplot2)
p <- ggplot(mtcars, aes(factor(cyl), mpg)) + geom_boxplot()
merge_pdf(2, file = "bar.pdf", widths = c(7, 10), heights = c(6, 10))
plot(1:10)
print(p)

Note that if you already have the pdfs you may want to look at the plotflow:::mergePDF function.

You can use sweave/knitr to get more flexibility and merge easily new plots ,old ones and texts:

\documentclass{article}
\usepackage{pdfpages}
\begin{document}
 this my plot 1:    % write some texts here
\includepdf{1.pdf} 
 this my plot 2:
\includepdf{2.pdf} 
 this my plot 3:
\includepdf{3.pdf} 
 this my plot 4:
\includepdf{4.pdf} 
 a new plot:
<<echo=FALSE>>=         % chunk for new plots
x <- rnorm(100)
hist(x)
@
\end{document}