plot.SpliceExprSet {splicegear} | R Documentation |
Plot a object of class SpliceExprSet
plot.SpliceExprSet(x, probes.opt = list(), expr.opt = list(col = NA, lty = 1:6), fig.xratio = c(2, 1), fig.yratio = c(2, 1), probepos.yscale = NULL, ylim, ...)
x |
a SpliceExprSet-class |
probes.opt |
optional parameters to be passed for the plotting of
the Probes-class |
expr.opt |
optional parameters to be passed for the plotting of
the exprSet-class |
fig.xratio |
ratio between the left and right parts of the plot |
fig.yratio |
ratio between the upper and lower parts of the plot |
probepos.yscale |
enforce `y' positions for the probes. |
ylim |
range for the y-axis |
... |
optional parameters to be passed to the function plot |
The argument probepos.yscale
can be used to scale probes
according to their position on the reference sequence, as shown
in the last example below.
function used for its side-effect(s).
laurent
data(spliceset) levels(pData(spliceset@eset)$Material) ## Liver, Mix and SNB19 cl.mat <- c("red", "yellow","blue")[as.integer(pData(spliceset@eset)$Material)] ## colored in red, yellow and blue respectively plot(spliceset, expr.opt = list(col = cl.mat, log = "x")) ## sort spliceset <- sort.SpliceExprSet(spliceset) begin.pos <- spliceset@probes@pos[, 1] plot(spliceset, expr.opt = list(col=cl.mat), probepos.yscale = begin.pos)