[Bioc-devel] question about affy::plotLocation - scripts

[James W. MacDonald]

Hi Kristóf,

On 6/16/2014 10:20 AM, Kristóf Jakab wrote:
> It seems I can't send attachments, I copy the codes here.
>
>
> test_plotLocation_affy.R
>
> #!/usr/bin/env Rscript
> #kristof.jakab at hegelab.org
>
> # MAKE AFFYBATCH
> #----------------------------------------------------------
> # download CEL file
> library(GEOquery)
> getGEOSuppFiles("GSM229005")
>
> #----------------------------------------------------------
> # read CEL file
> library(affy)
> geoS <- ReadAffy(filenames=paste("GSM229005","GSM229005.CEL.gz", sep="/"))
>
> # PLOTTING TO PNG
> #----------------------------------------------------------
> # raw
> png(filename="geo_testing_spot_locations_raw.png",height=744*10,width=744*10,res=1200)
>
> ## image (log scale intensities)
> image(geoS,transfo=log)
> ## perfectmatches
> l <- indexProbes(geoS, which="pm", geneNames(geoS))
> lapply(l,function(li){
>     xy <- indices2xy(li, abatch=geoS)
>     plotLocation(xy,col="tomato",pch=18,cex=0.075)
> })
> ## missmatches
> l <- indexProbes(geoS, which="mm", geneNames(geoS))
> lapply(l,function(li){
>     xy <- indices2xy(li, abatch=geoS)
>     plotLocation(xy,col="aquamarine",pch=18,cex=0.075)
> })
> dev.off()
>
> #----------------------------------------------------------
> # mirrored
> png(filename="geo_testing_spot_locations_mirrored.png",height=744*10,width=744*10,res=1200)
>
> ## image (log scale intensities)
> image(geoS,transfo=log)
> ## perfectmatches
> l <- indexProbes(geoS, which="pm", geneNames(geoS))
> lapply(l,function(li){
>     xy <- indices2xy(li, abatch=geoS)
>     xy <- cbind(x=xy[,1],y=(743-xy[,2])) # mirroring
>     plotLocation(xy,col="tomato",pch=18,cex=0.075)
> })
> ## missmatches
> l <- indexProbes(geoS, which="mm", geneNames(geoS))
> lapply(l,function(li){
>     xy <- indices2xy(li, abatch=geoS)
>     xy <- cbind(x=xy[,1],y=(743-xy[,2])) # mirroring
>     plotLocation(xy,col="aquamarine",pch=18,cex=0.075)
> })
> dev.off()
>
>
> correction_for_plotLocation.R
>
> plotLocation <- function(x, col="green", pch=22, ...) {
>     if (is.list(x)) {
>       x <- cbind(unlist(lapply(x, function(x) x[,1])),
>                  unlist(lapply(x, function(x) x[,2])))
>     }
>     points(x[,1], 743-x[,2] # mirroring 744Ã---744 matrix, numbered from 0 to 743
>            , pch=pch, col=col, ...)
> }

Thanks for pointing this out. It's apparent almost nobody ever uses this 
code, as it has been in the affy package since pretty much the beginning 
(2002), and you are the first to notice this.

Unfortunately, hard-coding the number of rows isn't the answer, since 
Affy arrays have different dimensions. Probably the best fix is to add 
an additional required argument 'affybatch' that we can use to extract 
the chip dimensions from.

Best,

Jim


>
>
> On 06/16/2014 10:59 AM, Kristóf Jakab wrote:
>> Dear BiocDevelR!
>>
>> I'm working lot with the excelent *affy package* of Rafael A.
>> Irizarry, I find it very useful.
>>
>> I have a bit strange experience with it's *plotLocation function*.
>> It seems, *I have to mirror Y coordinates* to plot properly.
>> Perhaps it's because the CEL file reading starts from the top, and
>> plotting starts from the bottom.
>>
>> I'm not sure if I'm rigtht, can you check, that I haven't made mistake?
>> If yes, I suggest a (simple) solution for this.
>>
>> I attach two plot made from a GEO GSM CEL file (see script).
>> First I've plotted all gene name (ProbeSet) on the CEL file images,
>> second I've plotted after mirroring the Y coordinates.
>> As you can see on the raw plotting there are points on chip name
>> (printed by BioB spots).
>>
>> I attach my plotting script too, and a potential correction for the
>> affy::plotLocation. (I've tried it, it seems good.)
>>
>> Yours sincerly:
>> Kristóf Jakab
>>
>> I've linked 2 files to this email:
>> geo_testing_spot_locations_mirrored.png
>> <https://www.box.com/shared/ow3q5sn3fpmyz3u8w533>(6.0 MB)Box
>> <https://www.box.com/thunderbird>https://www.box.com/shared/ow3q5sn3fpmyz3u8w533
>>
>> geo_testing_spot_locations_raw.png
>> <https://www.box.com/shared/3sj9i3lpkixkq85qar0r>(6.1 MB)Box
>> <https://www.box.com/thunderbird>https://www.box.com/shared/3sj9i3lpkixkq85qar0r
>>
>> Mozilla Thunderbird <http://www.getthunderbird.com> makes it easy to
>> share large files over email.
>
>
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>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099