RJaCGH (version 1.5.7)

genome.plot: Plot of the genome with probabilities of alteration.

Description

Plot of the genome showing, with a color key, the marginal probability of every gene of alteration.

Usage

genome.plot(obj, col = NULL, breakpoints = NULL, legend.pos=NULL,...)

Arguments

obj

An object of class RJaCGH.Chrom, RJaCGH.Genome or RJaCGH.array.

col

A vector of length k for the color of every range of probabilities of alteration, starting from loss to gain.

breakpoints

A vector of length k-1 for the breakpoints of the color key. The corresponding to losses must be negative. See example for details.

legend.pos

Position of the legend. Must be a vector with two elements; the position of the x and y coordinates. If NULL, the legend is placed at the right.

...

Aditional parameters passed to plot.

Value

• A plot is drawn.

Details

If col and breakpoints are NULL, a default color key is drawn.

References

Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122

Examples

data(snijders)
y <- gm13330$LogRatio[!is.na(gm13330$LogRatio)]
Pos <- gm13330$PosBase[!is.na(gm13330$LogRatio)]
Chrom <- gm13330$Chromosome[!is.na(gm13330$LogRatio)]

jp <- list(sigma.tau.mu=rep(0.05, 4), sigma.tau.sigma.2=rep(0.03, 4),
           sigma.tau.beta=rep(0.07, 4), tau.split.mu=0.1)
fit.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Genome",
burnin=1000, TOT=1000, jump.parameters=jp, k.max = 4)
genome.plot(fit.genome)
genome.plot(fit.genome, col=c(3, 1, 2), breakpoints=c(-0.5, 0.5))