plotGenome {aCGH} | R Documentation |
Plots the genome
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()
[Package
aCGH version 1.16.0
Index]