plotGenome {aCGH} | R Documentation |
Basic plot of the log2 ratios for each array ordered along the genome.
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")
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 |
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. |
#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()