%\VignetteIndexEntry{Plotting Idiograms}
%\VignetteKeywords{copy number, SNP}
%\VignettePackage{SNPchip}
\documentclass{article}
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\title{Plotting Idiograms}
\date{\today}

\author{Rob Scharpf}

\begin{document}
\maketitle

This package is no longer actively developed and maintained largely for historical reasons.

\section{Simple Usage}

<<packages, results=hide>>=
library(SNPchip)
@

Plot an idiogram for chromosome 1 with labels for the bands on the x-axis.

<<label=chr1, fig=TRUE, include=TRUE, width=12, height=2, results=hide>>=
plotIdiogram("1", build="hg19", cex=0.8)
@

Suppressing labels:

<<label=chr1NoLabels, fig=TRUE, include=TRUE, width=12, height=2, results=hide>>=
plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE)
@

With user-definded y-axis limits and y-coordinates for the idiogram:


<<label=differentCoordinates, fig=TRUE, include=TRUE, width=12, height=2, results=hide>>=
plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE, ylim=c(0,1), cytoband.ycoords=c(0.1, 0.3))
@

Plot an idiogram for all chromosomes.

<<allchrom,fig=TRUE,include=TRUE, width=10, height=6>>=
library(oligoClasses)
sl <- getSequenceLengths("hg19")[c(paste("chr", 1:22, sep=""), "chrX", "chrY")]
ybottom <- seq(0, 1, length.out=length(sl)) - 0.01
ytop <- seq(0, 1, length.out=length(sl)) + 0.01
for(i in seq_along(sl)){
	chr <- names(sl)[i]
	if(i == 1){
		plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE, ylim=c(-0.05,1.05), cytoband.ycoords=c(ybottom[1], ytop[1]),
			     xlim=c(0, max(sl)))
	}
	if(i > 1){
		plotIdiogram(names(sl)[i], build="hg19", cex=0.8, label.cytoband=FALSE, cytoband.ycoords=c(ybottom[i], ytop[i]), new=FALSE)
	}
}
axis(1, at=pretty(c(0, max(sl)), n=10), labels=pretty(c(0, max(sl)), n=10)/1e6, cex.axis=0.8)
mtext("position (Mb)", 1, line=2)
par(las=1)
axis(2, at=ybottom+0.01, names(sl), cex.axis=0.6)
@

\section{Session Information}

The version number of R and packages loaded for generating the vignette
were:

<<echo=FALSE, results=tex>>=
toLatex(sessionInfo())
@


\end{document}