[BioC] Colours in degradation plot

[kfbargad at lg.ehu.es]

Dear Jim,

thanks for your useful chunk of code. I pasted it and got some 
results, i.e, two different types of lines, but the command reached an 
erro and didn´t draw all the curves in my degradation plot. I had 27 
arrays and got only twelve lines, and the error I got is the following:

> my.plotAffyRNAdeg(AffyRNAdeg(data), col=1:length(sampleNames(data)))
Error in plot.xy(xy.coords(x, y), type = type, col = col, lty = 
lty, ...) : 
        invalid line type

I got eight solid lines and four ·-· lines

Can you give me some more hints?

Regards,

David



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