[SOLVED] Insert multiple images in for-loop into Sweave Document

Insert multiple images in for-loop into Sweave Document

I have five images stored as follows (where "currentDirectory" is the result I get from the command getwd()):

currentDirectory/results/thePlot_1.jpg
currentDirectory/results/thePlot_2.jpg
currentDirectory/results/thePlot_3.jpg
currentDirectory/results/thePlot_4.jpg
currentDirectory/results/thePlot_5.jpg

I am trying to write a .Rnw script in Rstudio that will create the .tex file that I can then run pdflatex on to have a .pdf file containing these five images. Below is what I have tried:

\documentclass{article}
\usepackage{float, hyperref}
\usepackage[margin=1in]{geometry}
\usepackage{graphicx}
\usepackage{hyperref}
\usepackage{caption}
\usepackage{algorithm}
\usepackage{algorithmic}

\begin{document}
\SweaveOpts{concordance=TRUE}

\author{myName}
\title{myTitle}

\maketitle

<<options, echo=FALSE>>=
library(knitr)
  opts_chunk$set(cache=TRUE)
@

\section*{mySection}

\FOR{i in 1:5}
nPlots=i
plotName = "thePlot"
outDir = "results"
\includegraphics{paste(getwd(), "/", outDir , "/", plotName, "_", i, sep="")}
\ENDFOR

\end{document}

For which I receive several errors:

Line 25: Undefined control sequence. Line 29: Missing $ inserted. Line 29: LaTeX Error: File `paste(getwd(), "/", outDir , "/", plotName, "_", i, sep="")' not found. Line 29: Missing $ inserted. Line 30: Undefined control sequence.

Any help greatly appreciated!

EDIT 1: I took into account Alex A.'s advice, and changed the section to include \Sexpr{} expressions as follows:

\FOR{i in 1:5}
\Sexpr{nPlots=i}
\Sexpr{plotName = "thePlot"}
\Sexpr{outDir = "results"}
\includegraphics{\Sexpr{paste(getwd(), "/", outDir , "/", plotName, "_", i, sep="")}}
\ENDFOR

\end{document}

However, I now receive an error:

object 'i' not found

I tried changing the condition in the for loop to also include \Sexpr{} as in:

\FOR{\Sexpr{i in 1:5}}

But this gets me the error:

Unexpected 'in'

Any help is appreciated!

EDIT 2:

I tried taking into account advice to simply put the for-loop and image-insertion into Rcode. So, I tried to use the jpeg library and its readJPEG method, as shown below:

<<echo=FALSE>>==
library(jpeg)
@

<<plots, echo = FALSE, fig = TRUE, figs.only = TRUE, results = hide>>=
for (i in 1:5){
  nPlots=i
  plotName = "thePlot"
  outDir = "results"

  img <- readJPEG(paste(getwd(), "/", outDir , "/", plotName, "_", i, ".jpg", sep=""))
  plot(img)
}
@

\end{document}

Unfortunately, this still leads to the error:

unexpected 'in'

Also, when I run the below code alone (not in the for-loop or .Rnw file):

  nPlots=1
  plotName = "thePlot"
  outDir = "results"

  img <- readJPEG(paste(getwd(), "/", outDir , "/", plotName, "_", i, ".jpg", sep=""))
  plot(img)

The image that generates looks different than the .jpeg image that I have (located in currentDirectory/results/thePlot_1.jpg)

Solution

From the Sweave Manual:

A.7 Creating several figures from one figure chunk does not work

Either save the plots manually and insert them using LaTeX includes (as recommended by the Sweave manual) or switch to knitr. I would recommend the latter.