[R] Need Help: User Defined R Functions in Sweave/Latex

[M. Jankowski]

Dear all,

I want to start my post by expressing my sincere gratitude for all the
help this group has given me in Sweave/Latex/R. The tools are
excellent and so is the community!

On to the question.

My Sweave code is intended to make lots of plots and create a *.pdf
document. Sweave is perfect for this. The only problem is that  I find
myself using the same R code, within my Sweave input file over an
over. I know about Latex macros and I can even get R functions,
essentially used as subroutines, to sort of work. "\Sexpr{}" will not
work because the R code I want to use over and over is in the R
environment. I've tried numerous ways to tackle this process and could
really use some help. If there is some easier way to do this please
let me know!

This is the R function:
basicplot <- function(x, nplots, sectionname){
# Begin to make figure here
file = paste("scatter",nplots, ".pdf", sep="")
pdf(file = file,paper="special", width=6, height = 6)
plot(x)
dev.off()
cat("\\begin{figure}\n")
cat("\\includegraphics{",file,"}\n", sep="")
cat("\\caption{", sectionname,"}\n", sep = "")
cat("\\end{figure}\n")
#End figure making
}

The aim is to generate Latex code which will have some basic
information as part of the caption. The trouble seems to be that the
output from the function appears to latex as if it is protected R code
when I really want to create output that pdflatex will act on.
Essentially, the resulting *.pdf contains the lines output by the cat
function in basicplot. Or:
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
These lines are not in the environment acted by Latex. I tried a
variant of the function where <<results=tex,echo=FALSE>> and received
the same result. Below are the files *.Snw -> *.tex -> *.pdf and the
output I received while compiling. If there is anything else I can
give to help you help me just let me know. Thanks!

Matt

My system:
T41 IBM Thinkpad
Ubuntu Feisty (7.04)
R version 2.5

testmacro3.Snw:
mdj at lapmdj:~/mydocs/R$ more testmacro3.Snw
\documentclass[a4paper]{article}
\usepackage{fullpage}
<<echo=f>>=
basicplot <- function(x, nplots, sectionname){
# Begin to make figure here
file = paste("scatter",nplots, ".pdf", sep="")
pdf(file = file,paper="special", width=6, height = 6)
plot(x)
dev.off()
cat("\\begin{figure}\n")
cat("\\includegraphics{",file,"}\n", sep="")
cat("\\caption{", sectionname,"}\n", sep = "")
cat("\\end{figure}\n")
#End figure making
}
@

\begin{document}
Filler text here.\\
<<>>=
library("flowCore")
x <- read.FCS("/home/mdj/data/yifacs2/NL7_PHA03_1.fcs", transformation = FALSE,
alter.names = TRUE);
basicplot(x, nplots = 1, sectionname="myname")
@
End text here \\
\end{document}

testmacro3.tex
\usepackage{/usr/share/R/share/texmf/Sweave}
\begin{document}
Filler text here.\\
\begin{Schunk}
\begin{Sinput}
> library("flowCore")
\end{Sinput}
\begin{Soutput}
Scalable Robust Estimators with High Breakdown Point (version 0.3-05)
\end{Soutput}
\begin{Sinput}
> x <- read.FCS("/home/mdj/data/yifacs2/NL7_PHA03_1.fcs", transformation = FALSE
,
+     alter.names = TRUE)
> basicplot(x, nplots = 1, sectionname = "myname")
\end{Sinput}
\begin{Soutput}
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
\end{Soutput}
\end{Schunk}
End text here \\
\end{document}

testmacro3.pdf:
Filler text here.
> library("flowCore")
Scalable Robust Estimators with High Breakdown Point (version 0.3-05)
> x <- read.FCS("/home/mdj/data/yifacs2/NL7_PHA03_1.fcs", transformation = FALSE,
+ alter.names = TRUE)
> basicplot(x, nplots = 1, sectionname = "myname")
\begin{figure}
\includegraphics{scatter1.pdf}
\caption{myname}
\end{figure}
End text here



Output:
mdj at lapmdj:~/mydocs/R$ R CMD Sweave testmacro3.Snw
[1] "Welcome to my custom R eenvironment!"
> library("utils"); Sweave("testmacro3.Snw")
Writing to file testmacro3.tex
Processing code chunks ...
 1 : term verbatim
 2 : echo term verbatim
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: rrcov
KernSmooth 2.22 installed
Copyright M. P. Wand 1997

You can now run LaTeX on 'testmacro3.tex'
> mdj at lapmdj:~/mydocs/Rpdflatex testmacro3.tex
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
entering extended mode
(./testmacro3.tex
LaTeX2e <2003/12/01>
Babel <v3.8d> and hyphenation patterns for american, french, german, ngerman, b
ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch, esperanto, e
stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk, polis
h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish, tur
kish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf-tetex/tex/latex/base/article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-tetex/tex/latex/base/size10.clo))
(/usr/share/texmf-texlive/tex/latex/preprint/fullpage.sty)
(/usr/share/R/share/texmf/Sweave.sty

LaTeX Warning: You have requested package `/usr/share/R/share/texmf/Sweave',
               but the package provides `Sweave'.

(/usr/share/texmf-tetex/tex/latex/base/ifthen.sty)
(/usr/share/texmf-tetex/tex/latex/graphics/graphicx.sty
(/usr/share/texmf-tetex/tex/latex/graphics/keyval.sty)
(/usr/share/texmf-tetex/tex/latex/graphics/graphics.sty
(/usr/share/texmf-tetex/tex/latex/graphics/trig.sty)
(/usr/share/texmf-tetex/tex/latex/graphics/graphics.cfg)
(/usr/share/texmf-tetex/tex/latex/graphics/pdftex.def)))
(/usr/share/texmf-texlive/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.6, with DG/SPQR fixes <1998/07/17> (tvz)
No file fancyvrb.cfg.
) (/usr/share/texmf/tex/latex/R/upquote.sty
(/usr/share/texmf-tetex/tex/latex/base/textcomp.sty
(/usr/share/texmf-tetex/tex/latex/base/ts1enc.def)))
(/usr/share/texmf-tetex/tex/latex/base/fontenc.sty
(/usr/share/texmf-tetex/tex/latex/base/t1enc.def))
(/usr/share/texmf-tetex/tex/latex/ae/ae.sty
(/usr/share/texmf-tetex/tex/latex/base/fontenc.sty
(/usr/share/texmf-tetex/tex/latex/base/t1enc.def)
(/usr/share/texmf-tetex/tex/latex/ae/t1aer.fd))))
No file testmacro3.aux.
(/usr/share/texmf-tetex/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-tetex/tex/context/base/supp-pdf.tex
(/usr/share/texmf-tetex/tex/context/base/supp-mis.tex
loading : Context Support Macros / Miscellaneous (2004.10.26)
)
loading : Context Support Macros / PDF (2004.03.26)
)
Underfull \hbox (badness 10000) in paragraph at lines 6--8

(/usr/share/texmf-tetex/tex/latex/ae/t1aett.fd)
Underfull \hbox (badness 10000) in paragraph at lines 26--27

[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./testmacro3.aux) )
(see the transcript file for additional information)</usr/share/texmf-tetex/fon
ts/type1/bluesky/cm/cmtt10.pfb></usr/share/texmf-tetex/fonts/type1/bluesky/cm/c
msltt10.pfb></usr/share/texmf-tetex/fonts/type1/bluesky/cm/cmr10.pfb>
Output written on testmacro3.pdf (1 page, 26713 bytes).
Transcript written on testmacro3.log.
mdj at lapmdj:~/mydocs/R$ xpdf testmacro3.pdf &
[4] 11100
mdj at lapmdj:~/mydocs/R$ Warning: Attempt to remove nonexistent passive grab
xpdf testmacro3.pdf &
[5] 11109
[4]   Done                    xpdf testmacro.pdf
mdj at lapmdj:~/mydocs/R$