data(sample.ExpressionSet)
## A bit of a hack to not have a package dependency on hgu95av2
## but need to fiddle w/ the warn level to not fail the example anyways.
curWarn <- options(warn=0)
on.exit(options(curWarn), add=TRUE)
if (require("hgu95av2.db")) {
z <- buildChromLocation("hgu95av2")
lty <- c(1, 2, 3, 4, 5)
cols <- c("red", "green", "blue", "orange", "magenta", "black")
cols <- cols[sample.ExpressionSet$type]
if (interactive()) {
par(ask=TRUE)
}
## Here we're using xlim to denote a physical region to display
xlim <- c(87511280,127717880)
for (xl in c("equispaced", "physical"))
for (sc in c("none","rangescale"))
{
alongChrom(sample.ExpressionSet, "1", z, xlim=xlim, xloc=xl,
plotFormat="cumulative", scale=sc,lty=lty, colors=cols)
}
## Here we're looking for specific genes
which <- c("31540_at","31583_at", "31508_at", "31529_at", "31439_f_at",
"31729_at")
## Gene "31529_at" does not exist in the current set of genes,
## here it demonstrates how genes not available are dropped.
for (xl in c("equispaced", "physical"))
for (sc in c("none","rangescale"))
{
alongChrom(sample.ExpressionSet, "1", z, which=which, xloc=xl,
plotFormat="cumulative", scale=sc,lty=lty, col=cols)
}
## Do an image plot
for (bs in c(TRUE,FALSE))
alongChrom(sample.ExpressionSet, "1",z, xlim=xlim, plotFormat="image",
scale="zscale", byStrand=bs)
## A boxplot
for (st in c(TRUE,FALSE))
alongChrom(sample.ExpressionSet, "1", z, plotFormat="local",
colors=cols, byStrand=st)
} else print("Example can not be run without the hgu95av2 data package")
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