kfbargad@lg.ehu.es wrote:
> Dear users,
>
> I am getting RNA degradation curves of 20 arrays, but the colours in
> the graph are repeated, so when I use the legend I cannot name them
> apart.
>
> I use col=1:length(names), and I only get 9 different colours, the
> colours are recicled, due to the default palette.
> What palette could I use for 20 or more arrays? I have tried other
> palettes but some of the colours are very difficult to separate
You will likely have a hard time using just colors to separate the
samples. Changing the line type is likely to work better for you.
Unfortunately, plotAffyRNAdeg() doesn't have a lty variable that you
can
use to change the line type. However, it is not difficult to add.
Something like the following might do the trick (although what I have
done here is hackish and ad hoc).
my.plotAffyRNAdeg <- function (rna.deg.obj, transform =
"shift.scale",
cols = NULL, lntype = NULL, ...)
{
if (!is.element(transform, c("shift.scale", "shift.only",
"neither")))
stop("Tranform must be 'shift.scale','shift.only', or
'neither'")
mns <- rna.deg.obj$means.by.number
if (is.null(cols))
cols = rep(4, dim(mns)[1])
ylab = "Mean Intensity"
if (transform == "shift.scale") {
sds <- rna.deg.obj$ses
mn <- mns[, 1]
mns <- sweep(mns, 1, mn)
mns <- mns/(sds)
mns <- sweep(mns, 1, 1:(dim(mns)[1]), "+")
ylab <- paste(ylab, ": shifted and scaled")
}
else if (transform == "shift.only") {
mn <- mns[, 1]
mns <- sweep(mns, 1, mn)
mns <- sweep(mns, 1, 1:(dim(mns)[1]), "+")
ylab <- paste(ylab, ": shifted")
}
plot(-2, -1, pch = "", xlim = range(-1, (dim(mns)[2])), ylim =
range(min(as.vector(mns)) -
1, max(as.vector(mns)) + 1), xlab = "5' <-----> 3'\n Probe
Number ",
ylab = ylab, axes = FALSE, main = "RNA digestion plot",
...)
axis(1)
axis(2)
if(is.null(lntype)){
full <- floor(dim(mns)[1]/8)
mod <- dim(mns)[1]%%8
for(i in (seq(along=full)))
lntype <- c(lntype, rep(i, 8))
lntype <- c(lntype, rep(full + 1, mod))
}
for (i in 1:dim(mns)[1]) lines(0:((dim(mns)[2] - 1)), mns[i,
], col = cols[i], lty = lntype[i])
}
Paste this into your R session, then you can do something like:
my.plotAffyRNAdeg(AffyRNAdeg(abatch),
col=1:length(sampleNames(abatch)))
HTH,
Jim
>
> thanks in advance,
>
> David
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
>
https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
