[BioC] Colours in degradation courve

[James W. MacDonald]

kfbargad at 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
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109