[BioC] Geneplotter, alongChrom problem

[Wolfgang Huber]

Hi Giulio,

try

alongChrom(eset, "Y", newChrom, xloc = "equispaced",
   plotFormat = "image", scale = "zscale", colors = cm.colors(256))

It seems that the default value of the 'colors' parameter (namely, just 
the single value "red"), is not good for the image plot format.

   Cheers,
    Wolfgang

Giulio Di Giovanni wrote:
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber