[Bioc-devel] [R-SIG-Mac] splots -- svn commit plotScreen.R - CORRECTED

Fri Sep 15 01:09:01 CEST 2006

The following modification has been introduced. The code committed to 
BioC svn as revision 19830, please update. The tarball will take several 
days until the build system runs through. Thanks all for pointing out to 
the solution:

80: grid.rect(0.5, 0.5, 1, 1, gp = gpar(col = abris, fill = "transparent"))

Best,
Oleg

Steven McKinney wrote:
> Thanks very much Simon,
> 
> Your suggested fix works for my situation.
> 
> After changing
> 
> grid.rect(0.5, 0.5, 1, 1, gp = gpar(col = abris))
> 
> to
> 
> grid.rect(0.5, 0.5, 1, 1, gp = gpar(col = abris, fill="transparent"))
> 
> in plotScreen(), I get a proper rendering of the
> demo graphic in the Quartz window using R.app.
> 
> 
> 
> Best regards
> 
> Steven McKinney
> 
> Statistician
> Molecular Oncology and Breast Cancer Program
> British Columbia Cancer Research Centre
> 
> email: smckinney at bccrc.ca
> 
> tel: 604-675-8000 x7561
> 
> BCCRC
> Molecular Oncology
> 675 West 10th Ave, Floor 4
> Vancouver B.C. 
> V5Z 1L3
> Canada
> 
> 
> 
> 
> -----Original Message-----
> From: Simon Urbanek [mailto:simon.urbanek at r-project.org]
> Sent: Thu 9/14/2006 1:31 PM
> To: Steven McKinney; Paul Murrell
> Cc: Bioc-devel at stat.math.ethz.ch; R SIG Mac List
> Subject: Re: [R-SIG-Mac] splots -- new package announcement
>  
> 
> On Sep 14, 2006, at 4:20 PM, Simon Urbanek wrote:
> 
>> On Sep 14, 2006, at 3:23 PM, Steven McKinney wrote:
>>
>>> Forwarding to r-sig-mac
>>>
>>> Anyone else have problems with the Quartz graphics display
>>> generated from R.app, running the example from new package 'splots' ?
>>>
>> IMHO it's a bug in splots:
>>
>> grid.rect(0.5, 0.5, 1, 1, gp = gpar(col = abris))
>> ^-- this will fill the whole area with the default fill color which
>> is white:
>>> get.gpar()$fill
>> [1] "white"
>>
>> I guess it should read
>> grid.rect(0.5, 0.5, 1, 1, gp = gpar(col = abris, fill=NULL))
>>
> 
> Actually it should be fill="transparent" I presume [gpar(fill=NULL)  
> returns an empty list despite the docs indicating otherwise .. hmm...  
> an issue with grid as well?].
> 
> Cheers,
> Simon
> 
>>> -----Original Message-----
>>> From: bioc-devel-bounces at stat.math.ethz.ch on behalf of Steven
>>> McKinney
>>> Sent: Wed 9/13/2006 12:21 PM
>>> To: Oleg Sklyar; bioc-devel at stat.math.ethz.ch
>>> Subject: Re: [Bioc-devel] splots -- new package announcement
>>>
>>> Hi Oleg,
>>>
>>> As I have some 96 well plate data to look at
>>> right now, I downloaded your package.
>>>
>>> Unfortunately I am having trouble on
>>> Mac OS X 10.4.7 and Rapp 2.3.1
>>>
>>> If I run your example,
>>>
>>>> data(splots.screen)
>>>> plotScreen(screen, 3)
>>> I get a Quartz screen with 12 grey
>>> rectangles, subtitled 'datasetnn',
>>> (nn = 1, 2, ... 12)
>>> all white otherwise.
>>>
>>> If I resize the screen, I briefly see coloured
>>> rectangles within the grey borders, but then white
>>> returns and all is blank.
>>>
>>> I also tried printing to a PDF file, which worked
>>> properly, so I can at least do that.
>>>
>>> Anyone have similar problems with other plots?
>>> Is this an Rapp/Quartz issue only?  Have I set up
>>> something inappropriately?
>>>
>>> Any insights appreciated.
>>>
>>>
>>>
>>>
>>>
>>>
>>>> version
>>>                _
>>> platform       powerpc-apple-darwin8.6.0
>>> arch           powerpc
>>> os             darwin8.6.0
>>> system         powerpc, darwin8.6.0
>>> status
>>> major          2
>>> minor          3.1
>>> year           2006
>>> month          06
>>> day            01
>>> svn rev        38247
>>> language       R
>>> version.string Version 2.3.1 (2006-06-01)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Steven McKinney
>>>
>>> Statistician
>>> Molecular Oncology and Breast Cancer Program
>>> British Columbia Cancer Research Centre
>>>
>>> email: smckinney at bccrc.ca
>>>
>>> tel: 604-675-8000 x7561
>>>
>>> BCCRC
>>> Molecular Oncology
>>> 675 West 10th Ave, Floor 4
>>> Vancouver B.C.
>>> V5Z 1L3
>>> Canada
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: bioc-devel-bounces at stat.math.ethz.ch on behalf of Oleg Sklyar
>>> Sent: Wed 9/13/2006 7:32 AM
>>> To: bioc-devel at stat.math.ethz.ch
>>> Subject: [Bioc-devel] splots -- new package announcement
>>>
>>> Hi all,
>>>
>>> a couple of weeks ago I submitted a yet tiny new package, splots,  
>>> that
>>> aims to deliver different plotting routines for high-throughput
>>> screens
>>> independently of analysis packages. The idea is too have a separate
>>> plotting package with a minimum dependencies that would allow for  
>>> nice
>>> plots of screen-like data (what is currently done by parts of  
>>> cellHTS,
>>> prada etc).
>>>
>>> The package has now passed through build/check and therefore I am
>>> announcing it.
>>>
>>> At the moment, the package contains one single function, plotScreen,
>>> which is a grid-graphics implementation of a similar function from
>>> cellHTS (credit to Ligia Breas for the idea!), and it stays this
>>> way for
>>> the release. However I will add a couple of functions in the later
>>> devel
>>> version as time allows.
>>>
>>> I would be really happy if the package attract not only users but
>>> developers as well. Feel free to participate in package development,
>>> adding new functions, or simply using it.
>>>
>>> Best,
>>> Oleg
>>>
>>> -- 
>>> Dr. Oleg Sklyar | EBI, Cambridge CB10 1SD, England | +44-1223-494466
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> _______________________________________________
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>>>
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>>>
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>>
> 
> 
> 

-- 
Dr. Oleg Sklyar
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
England

Tel   +44-1223-494466
Fax   +44-1223-494468
email osklyar at ebi.ac.uk