[BioC] Geneplotter, alongChrom problem

[Giulio Di Giovanni]

Hi to all,

I have a problem using alongChrom in Geneplotter pkg, with the "image" plot.
With this type of plot, all that I obtain is a single color filled image, 
instead the multicolor image. I didn't receive any error messages.

I tried with different expression set and for different chromosomes, but 
with no differences. For example, the run from commonly known  "An 
introduction to some graphics in Bioconductor" pdf document is:


>library(annotate)
>library(geneplotter)
>library(hgu95av2)
>data(eset)
>newChrom <- buildChromLocation("hgu95av2")
>newChrom
Instance of a chromLocation class with the following fields:
        Organism:  Homo sapiens
        Data source:  hgu95av2
        Number of chromosomes for this organism:  25
        Chromosomes of this organism and their lengths in base pairs:
                 1 : 246127941
                 2 : 243615958
                 3 : 199344050
                 4 : 191731959
                 5 : 181034922
                 6 : 170914576
                 7 : 158545518
                 8 : 146308819
                 9 : 136372045
                 10 : 135037215
                 11 : 134482954
                 12 : 132078379
                 13 : 113042980
                 14 : 105311216
                 15 : 100256656
                 16 : 90041932
                 17 : 81860266
                 18 : 76115139
                 19 : 63811651
                 20 : 63741868
                 21 : 46976097
                 22 : 49396972
                 X : 153692391
                 Y : 50286555
                 M : 16571
>
>par(mfrow = c(2, 1))
>for (sc in c("max", "relative")) cPlot(newChrom, fg = "blue",
+ scale = sc)
>
>cols <- c("red", "green", "blue")
>cols <- cols[eset$cov3]    # needs eset - expression set
>par(mfrow = c(3, 2))
>alongChrom(eset, "1", newChrom, xloc = "equispaced", plotFormat = 
>"cumulative",
+ col = cols, lwd = 2)
<environment: 027EDB48>
>alongChrom(eset, "1", newChrom, xloc = "physical", col = cols,
+ lwd = 2)
<environment: 021B72B4>
>alongChrom(eset, "1", newChrom, xloc = "equispaced", plotFormat = "local",
+ col = cols, lwd = 2)
>alongChrom(eset, "1", newChrom, xloc = "equispaced", plotFormat = "local",
+ col = cols, type = "p", pch = 16)
>alongChrom(eset, "1", newChrom, xlim = c(87511280, 127717880),
+ xloc = "equispaced", plotFormat = "local", col = cols, type = "p",
+ pch = 16)
>alongChrom(eset, "Y", newChrom, xloc = "equispaced", plotFormat = "image", 
>scale="zscale")
>

All the plots are OK, but the last one as I said is a completly red image...
I have the same result for all the datasets that I tried...

Please, someone could suggest me what I'm doing wrong ?

Thank you to all in advance,

Giulio