[BioC] Colours in degradation plot

[James W. MacDonald]

kfbargad at lg.ehu.es wrote:
> 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?

Stupid mistake on my part. Change the line in my.plotAffyRNAdeg() near 
the end that reads:

for(i in (seq(along=full)))
	lntype <- c(lntype, rep(i, 8))

-to-

for(i in 1:full)
	lntype <- c(lntype, rep(i, 8))

Then it should work.

Jim


> 
> 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
> 
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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