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

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

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.