plotGenome: Plots the genome

Description Usage Arguments See Also Examples

View source: R/aCGH.plotting.R

Description

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

Usage

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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

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#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()

Bioconductor-mirror/aCGH documentation built on June 1, 2017, 4:13 a.m.