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: [EMAIL PROTECTED] > > 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:[EMAIL PROTECTED] > Sent: Thu 9/14/2006 1:31 PM > To: Steven McKinney; Paul Murrell > Cc: [EMAIL PROTECTED]; 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: [EMAIL PROTECTED] on behalf of Steven >>> McKinney >>> Sent: Wed 9/13/2006 12:21 PM >>> To: Oleg Sklyar; [EMAIL PROTECTED] >>> 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: [EMAIL PROTECTED] >>> >>> tel: 604-675-8000 x7561 >>> >>> BCCRC >>> Molecular Oncology >>> 675 West 10th Ave, Floor 4 >>> Vancouver B.C. >>> V5Z 1L3 >>> Canada >>> >>> >>> >>> >>> -----Original Message----- >>> From: [EMAIL PROTECTED] on behalf of Oleg Sklyar >>> Sent: Wed 9/13/2006 7:32 AM >>> To: [EMAIL PROTECTED] >>> 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 >>> >>> _______________________________________________ >>> [EMAIL PROTECTED] mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> _______________________________________________ >>> [EMAIL PROTECTED] mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> > > > -- Dr. Oleg Sklyar European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD England Tel +44-1223-494466 Fax +44-1223-494468 email [EMAIL PROTECTED] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
