[BioC] GenomeGraphs plot colours (bug?)

Tim Rayner tfrayner at gmail.com
Tue Feb 24 16:24:39 CET 2009


I'm using the GenomeGraphs package to plot expression data for
multiple sample groups, and I've run into something that may or may
not be classed as a bug. I've been using
DisplayPars(color=c('blue','red')) to visually differentiate between
sample groups, and that works well under most circumstances. However,
I've found that when using e.g. makeGenericArray() that the addition
of a probeEnd argument renders the graph using only the first colour
in the DisplayPars list. Example code and sessionInfo() attached
below. I only noticed this because I happened to try using
DisplayPars(type="line") with probeStart and probeEnd to indicate the
length of the interrogated genome region on the plots. Aside from this
minor niggle, nice package!


Tim Rayner

## Example code follows:
testGenomePlot <- function () {


    data("exampleData", package = "GenomeGraphs")
    minBase <- 180292097
    maxBase <- 180492096

    ## Replace the default intensity data for example's sake (we need
two samples)
    intensity <- matrix(rnorm(184), ncol=2)

    expres <- makeGenericArray(intensity = intensity,
                               probeStart = exonProbePos,
                               dp = DisplayPars(
                                 color = c("blue","red"),
                                 type = "point",
    expres2 <- makeGenericArray(intensity = intensity,
                               probeStart = exonProbePos,
                               probeEnd = exonProbePos+200,  # different
                               dp = DisplayPars(
                                 color = c("blue","red"),
                                 type = "point",

    gdPlot(list(good=expres, bad=expres2),
           minBase = minBase,
           maxBase = maxBase)



R version 2.8.1 Patched (2009-01-19 r47650)


attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomeGraphs_1.2.3 biomaRt_1.16.0

loaded via a namespace (and not attached):
[1] RCurl_0.94-1 XML_1.99-0   tools_2.8.1

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