%\VignetteIndexEntry{OOMPA}
%\VignetteKeywords{OOMPA}
%\VignetteDepends{oompaBase}
%\VignettePackage{oompaBase}
\documentclass{article}

\usepackage{hyperref}
\usepackage{Sweave}

\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Robject}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}
\newcommand{\Rclass}[1]{{\textit{#1}}}

\title{Object Oriented Microarray and Proteomics Analysis (OOMPA)}
\author{Kevin R. Coombes}

\begin{document}

\maketitle
\tableofcontents

\section{Introduction}

OOMPA is a suite of object-oriented tools for processing and analyzing
large biological data sets, such as those arising from mRNA expression
microarrays or mass spectrometry proteomics.

This vignette documents the base package, \Rpackage{oompaBase}.  A
critical (but invisible to the user) feature of the
\Rpackage{oompaBase} package is that it defines a 
\Robject{class union} allowing you to use ``numeric'' or ``NULL''
objects in the design of an S4 class.  More interesting user-visible
features include alternative color schemes and vectorized matrix
operations to speed the computation of row-by-row means, variances,
and t-tests. 

\section{Getting Started}

You invoke the package in the usual way:
<<invoke>>=
library(oompaBase)
@ 

\section{Color Schemes}

To illustrate the various color schemes, we first create a structured
matrix: 
<<data>>=
mat <- matrix(1:1024, ncol=1)
@ 
The following code is used to generate Figure~\ref{colsch}.
<<figmaker,eval=FALSE>>=
# windows(width=6,height=8)
opar <- par(mfrow=c(8, 1), mai=c(0.3, 0.5, 0.2, 0.2))
image(mat, col=jetColors(128), main='jetColors')
image(mat, col=wheel(64, 0.5), main='wheel, half saturation')
image(mat, col=redgreen(64), main='redgreen')
image(mat, col=blueyellow(32), main='blueyellow')
image(mat, col=cyanyellow(32), main='cyanyellow')
image(mat, col=redscale(64), main='redscale')
image(mat, col=bluescale(64), main='bluescale')
image(mat, col=greyscale(64), main='greyscale')
par(opar)
@ 

\begin{figure}
<<fig=TRUE,echo=FALSE,width=6,height=8>>=
<<figmaker>>
@ 
\caption{Eight color schemes.}
\label{colsch}
\end{figure}

\section{Row-by-row Matrix Operations}

We now want to illustrate the ``matrix operations'' that allow for
rapid computation of row-by-row means, variances, and t-tests.

We start by creating a slightly more interesting matrix full of random
data.  First, we make the variance larger in the second half (by
column) of the data than in the first half.
<<dat>>=
ng <- 10000
ns <- 50
dat <- matrix(rnorm(ng*ns, 0, rep(c(1, 2), each=25)), ncol=ns, byrow=TRUE)
@ 
Next, we shift the mean for the first $500$ ``genes'' (rows).
<<dat>>=
dat[1:500, 1:25] <- dat[1:500, 1:25] + 2
@ 
In order to compute t-tests, we also assign arbitrary labels
separating the ``sample columns'' into two groups.
<<clas>>=
clas <- factor(rep(c('Good', 'Bad'), each=25))
@ 

Here we compute the row-by-row means.
<<mm>>=
a0 <- proc.time()
myMean <- matrixMean(dat)
used0 <- proc.time() - a0
@ 
For comparison purposes, we perfom the same computation using
\Rfunction{apply}.
<<checkApply>>=
a1 <- proc.time()
mm <- apply(dat, 1, mean)
used1 <- proc.time() - a1
@ 
The results are the same, to within round-off error.
<<nodiff>>=
summary(as.vector(myMean-mm))
@ 
There is a measurable (although not really user-perceptible)
difference in the time for the two methods.
<<times>>=
used0
used1
@ 

Here we compute the variances using two different methods.
<<varns>>=
a0 <- proc.time()
myVar  <- matrixVar(dat, myMean)
a1 <- proc.time()
vv <- apply(dat, 1, var)
a2 <- proc.time()
@ 
Again, the values are the same:
<<nodiffv>>=
summary(as.vector(myVar - vv))
@ 

However, the time savings is substantially larger.
<<timers>>=
a1 - a0
a2 - a1
@ 

Not surprisingly, there is an even bigger time savings when computing
(equal variance) t-statistics.
<<tstats>>=
t0 <- proc.time()
myT <- matrixT(dat, clas)
t1 <- proc.time()
tt <- sapply(1:nrow(dat), function(i) {
  t.test(dat[i,clas=="Bad"], dat[i, clas=="Good"], var.equal=T)$statistic
})
t2 <- proc.time()
@ 
<<>>=
summary(as.vector(tt - myT))
@ 
<<>>=
t1 - t0
t2 - t1
@ 

\section{Color Coded Graphs}

We frequently find ourselves producing multiple figures with a common
color scheme, where each color or each symbol is used to denote
samples or genes with a particular property (in the simplest case,
``cancer'' versus ``normal'').  Because we got tired of continually
cutting and pasting \Rfunction{plot} and \Rfunction{points} commands
and making sure the color legends stayed synchronized, we developed
the \Rclass{ColorCoding} and \Rclass{ColorCodedPair} classes to
encapsulate this notion.

We can simulate some data as an example.
<<xy>>=
x <- matrix(rnorm(100*3), nrow=100, ncol=3)
class1 <- class2<- rep(FALSE, 100)
class1[sample(100, 20)] <- TRUE
class2[sample(100, 20)] <- TRUE
class3 <- !(class1 | class2)
codes <- list(ColorCoding(class1, "red", 16),
              ColorCoding(class2, "blue", 15),
              ColorCoding(class3, "black", 17))
@ 
\begin{figure}
<<pcc,fig=TRUE,width=6,height=8>>=
par(mfrow=c(2,1))
plot(ColorCodedPair(x[,1], x[,2], codes), xlab="Coord1", ylab="Coord2")
plot(ColorCodedPair(x[,1], x[,3], codes), xlab="Coord1", ylab="Coord3")
par(mfrow=c(1,1))
@ 
\caption{Color coded plots of three (simulated) related variables.}
\label{fig:pcc}
\end{figure}



\end{document}
