[BioC] Geneplotter, alongChrom problem solved

[Giulio Di Giovanni]

Now it's ok. So, alongChrom require the multi-colors selection...

Thanks a lot !

Giulio

>From: Wolfgang Huber <huber at ebi.ac.uk>
>To: Giulio Di Giovanni <perimessaggini at hotmail.com>
>CC: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Geneplotter, alongChrom problem
>Date: Tue, 22 Mar 2005 22:47:36 +0100
>
>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
>-------------------------------------