plotGenome: Plots the genome

In aCGH: Classes and functions for Array Comparative Genomic Hybridization data

Description

Basic plot of the log2 ratios for each array ordered along the genome.

Usage

plotGenome(aCGH.obj, samples = 1:num.samples(aCGH.obj), naut = 22,
           Y = TRUE, X = TRUE, data = log2.ratios(aCGH.obj),
           chrominfo = human.chrom.info.Jul03,
           yScale = c(-2, 2), samplenames = sample.names(aCGH.obj),
           ylb = "Log2Ratio")

Arguments

aCGH.obj	an object of class aCGH
samples	vector containing indeces of the samples to be plotted.
naut	number of autosomes in the organism
Y	TRUE if chromosome Y is to be plotted, FALSE otherwise
X	TRUE if chromosome X is to be plotted, FALSE otherwise
data	a matrix containing values to use for plotting. defaults to the log2.ratios(aCGH.obj).
chrominfo	a chromosomal information associated with the mapping of the data.
yScale	Minimum y-scale to use for plotting. Scale is expanded if any of the values exceed the positive or negative limit.
samplenames	sample names.
ylb	label for the Y-axis.

See Also

aCGH

Examples

#plot samples in the order of descending quality 
data(colorectal)
order.quality <- order(sd.samples(colorectal)$madGenome)
pdf("plotGenome.orderByQuality.pdf")
par(mfrow=c(2,1))
for(i in order.quality)
   plotGenome(colorectal, samples = i, Y = FALSE)
dev.off()

aCGH documentation built on Nov. 8, 2020, 6:58 p.m.