Why?

July 13, 2012

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays

Filed under: latex, Microarray, Publications, R — Tags: , , — csgillespie @ 2:32 pm

A few years ago I was involved in analysing some time-course microarray data. Our biological collaborators were interested in how we analysed their data, so this lead to a creation of tutorial, which in turn lead to a paper. When we submitted the paper, one the referees “suggested” that we write the paper using Sweave; I had never used Sweave. At the time this was a massive pain and I regularly cursed the name of the anonymous referee.  A few years later, I’ve just updated code (due to a change in Bioconductor) and it was a breeze. A belated thanks to the referee.

In this latest update to the paper I’ve

  • moved the paper to github;
  • changed from Sweave to knitr;
  • used RStudio instead of emacs.

You can find details full details about analysis on the associated github page.

May 12, 2011

Makefiles and Sweave

Filed under: Computing, latex, R — Tags: , , , , — csgillespie @ 8:19 pm

A Makefile is a simple text file that controls compilation of a target file. The key benefit of using Makefile is that it uses file time stamps to determine if a particular action is needed. In this post we discuss how to use a simple Makefile that compiles a tex file that contains a number of \include statements. The files referred to by the \include statements are Sweave files.

Suppose we have a master tex file called master.tex. In this file we have:

\include chapter1
\include chapter2
\include chapter3
....

where the files chapter1, chapter2, chapter3 are Sweave files. Ideally, when we compile master.tex, we only want to sweave if the time stamp of chapter1.tex is older than the time stamp of chapter1.Rnw. This conditional compiling is even more important when we have a number of sweave files.

Meta-rules

To avoid duplication in a Makefile, it’s handy to use meta-rules. These rules specify how to convert from one file format to another. For example,

.Rnw.tex:
    R CMD Sweave $<

is a meta rule for converting an Rnw file to a tex file. In the above meta-rule, $< is the filename, i.e. chapter1.Rnw. Other helpful meta rules are:

.Rnw.R:
    R CMD Stangle $<

which is used to convert between Rnw and R files. We will also have a meta-rule for converting from .tex to .pdf.

For meta-rules to work, we have to list all the file suffixes that we will convert between. This means we have to include the following line:

.SUFFIXES: .tex .pdf .Rnw .R

Files to convert

Suppose we have a master tex file called master.tex and a sweave file chapter1.Rnw. This means we need to convert from:

  • master.tex to master.pdf
  • chapter1.Rnw to chapter1.tex
  • chapter1.Rnw to chapter1.R

Obviously, we don’t want to write down every file we need – especially if we have more than one sweave file. Instead, we just want to state the master file and the Rnw files. There are a couple of ways of doing this, however, the following way combines flexibility and simplicity. We first define the master and Rnw files:


##Suppose we have three Sweave files with a single master file
MAIN = master
RNWINCLUDES = chapter1 chapter2 chapter3

Now we add in the relevant file extensions

TEX = $(RNWINCLUDES:=.tex)
RFILES = $(RNWINCLUDES:=.R)
RNWFILES = $(INCLUDES:=.Rnw)

In the Makefile, whenever we use the $(TEX) variable, it is automatically expanded to

chapter1.tex chapter2.tex chapter3.tex

A similar rule applies to $(RFILES) and $(RNWFILES).

Conversion rules

We now define the file conversion rules. When we build our pdf file we want to:

  • build the tex file from Rnw file only if the Rnw files have changed or if the tex file doesn’t exist.
  • build the pdf file from the tex file only if master.tex file has changed or one of the Rnw files has changed, or the pdf file doesn’t exist.

We can accomplish this with the following rule:

$(MAIN).pdf: $(TEX) $(MAIN).tex

Typically, I also have a dependencies on a graphics directory and a bibtex file

$(MAIN).pdf: $(TEX) $(MAIN).tex refs.bib graphics/*.pdf

We also have a conversion rule to R files.

R: $(RFILES)

Cleaning up

We also use sweave to clean up after ourselves:

clean:
rm -fv $(MAIN).pdf $(MAIN).tex $(TEX) $(RFILES)
rm -fv *.aux *.dvi *.log *.toc *.bak *~ *.blg *.bbl *.lot *.lof
rm -fv *.nav *.snm *.out *.pyc \#*\# _region_* _tmp.* *.vrb
rm -fv Rplots.pdf *.RData

The complete Makefile

In the Makefile below:

  • make all – creates master.pdf;
  • make clean – deletes all files created as part of the latex and sweave process;
  • make R – creates the R files from the Rnw files.

.SUFFIXES: .tex .pdf .Rnw .R

MAIN = master
RNWINCLUDES = chapter1 chapter2 chapter3
TEX = $(RNWINCLUDES:=.tex)
RFILES = $(RNWINCLUDES:=.R)
RNWFILES = $(INCLUDES:=.Rnw)

all: $(MAIN).pdf
    $(MAIN).pdf: $(TEX) $(MAIN).tex

R: $(RFILES)

view: all
    acroread $(MAIN).pdf &

.Rnw.R:
    R CMD Stangle $<

.Rnw.tex:
    R CMD Sweave $<

.tex.pdf:
    pdflatex $<
    bibtex $*
    pdflatex $<
    pdflatex $<

clean:
    rm -fv $(MAIN).pdf $(MAIN).tex $(TEX) $(RFILES)
    rm -fv *.aux *.dvi *.log *.toc *.bak *~ *.blg *.bbl *.lot *.lof
    rm -fv *.nav *.snm *.out *.pyc \#*\# _region_* _tmp.* *.vrb
    rm -fv Rplots.pdf *.RData

Useful links

  • Jeromy Anglim’s post on Sweave and Make;
  • Ross Ihaka’s Makefile on Sweave;
  • Instead of using a Makefile, you could also use a shell script;

December 8, 2010

LaTeX doodle pad

Filed under: Geekery, latex — Tags: , — csgillespie @ 8:59 pm

Every so often you’re typing away at a tex document and you have forgotten the latex command. You don’t have any latex books with you and using Google to find a latex symbol is a lesson in frustration. Don’t worry detexify is at hand. Just doodle your symbol in the box and up pops a few suggestions.

Here’s my attempt at drawing nleftarrow

Very useful!

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