[Bioc-devel] [R-SIG-Mac] splots -- new package announcement

[Steven McKinney]

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
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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