splots -- svn commit plotScreen.R - CORRECTED
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
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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