13_MicroArrayHeatMap.rnw

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\begin{document}
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\begin

<<setup, include=FALSE, cache=FALSE>>=
library(knitr)
# set global chunk options
opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold')
options(replace.assign=TRUE,width=90)
@


\title{Array Expression Data Analysis report}


\author{Vikas Gupta, Niraj Shah and Stig U. Andersen}

\maketitle
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\tableofcontents
\newpage


<<SNP destribution Sliding Window>>=

d <- read.table('~/Desktop/temp/1kb.ld', header = T)
head(d)
plot(d$L1, d$L2)

@

\newline 

% add dot after number
\makeatletter
\g@addto@macro\thesection.
\makeatother

\section{Introduction}


\section{WorkFlow}

<< Installation , cache=TRUE>>=

source("http://www.bioconductor.org/biocLite.R")
biocLite("ALL")

@

<< Load data , cache=TRUE >>=
library('ALL')
data('ALL')
@


<< Process data , cache=TRUE >>=
ALL
ALL$mol.biol
eset <- ALL[, ALL$mol.biol %in% c("BCR/ABL", "ALL1/AF4")]
heatmap(exprs(eset[1:100,]))

@

<< testing >>=
mat <- matrix(c(1,2,NA,2,1,4),nrow=3,ncol=2)
heatmap(mat, col=topo.colors(100), Colv = NULL, na.rm=T)

@

<< Load the data >>=
jpeg("~/Desktop/03_Lotus_annotation/2013_week44/04_genelist.txt.arrayData.jpg", width=2600, 
     height=1800, quality=90, units="px")
d <- read.table('~/Desktop/03_Lotus_annotation/2013_week44/04_genelist.txt.arrayData', header=T)
#d_all <- read.table('~/Desktop/03_Lotus_annotation/2013_week44/export_2013-11-04-02-43-41_5411.txt.means', header=T)
#head(d)
#names(d)
#plot(d$Mean_WT_control1, d$Std_WT_control1)
#plot(d_all$Mean_WT_control1, d_all$Std_WT_control1, col='red')
#length(which(d_all$Std_WT_control1/d_all$Mean_WT_control1 >0.2))
par(mfcol=c(1,1), mar=c(2.5,2.5,2.5,2.5), oma=c(25,1,1,80))
d2 <- as.matrix(d[,])
# seed - lightblue
# pod - blue
# flower - yellow
# shoot - green
# petiole - pink
# leaf - violet
# stem - white
# root - gray
# nodules - red
# nodules+root - orange

colors <- c(rep("lightblue",length = 5), 
            rep("blue",length = 1), 
            rep("yellow",length = 2), 
            rep("green",length = 30), 
            rep("pink",length = 1), 
            rep("violet",length = 2), 
            rep("white",length = 2), 
            rep("gray",length = 28), 
            rep("red",length = 5), 
            rep("orange",length = 2))
heatmap(d2, labRow = rownames(d), labCol = c(colnames(d)), col=topo.colors(100), keep.dendro = FALSE, Colv = NA , cex.axis=0.1,  pch=10, cex.lab=1.1,cexRow=2.5, cexCol=1.5, ColSideColors=colors)
dev.off()
@

\section{Plotting}


\end{document}