From hin-tak.leung at cimr.cam.ac.uk  Fri Jul 21 18:45:40 2006
From: hin-tak.leung at cimr.cam.ac.uk (Hin-Tak Leung)
Date: Fri, 21 Jul 2006 17:45:40 +0100
Subject: [Rd] png() and image()
In-Reply-To: <59d7961d0607201855x37b2fb3bw6d89939e1409287d@mail.gmail.com>
References: <59d7961d0607201855x37b2fb3bw6d89939e1409287d@mail.gmail.com>
Message-ID: <44C104B4.50105@cimr.cam.ac.uk>

By changing
   png("large.png", height=nrow(z), width=ncol(z), bg="red")
to
   png("large.png", height=nrow(z), width=ncol(z), bg="blue")
I can get the right column (on linux) to change to blue.

So it seems to be an alignment off-by-one error with the background
colour showing through, so you might be able to work around it
by changing the alignment of the margins.

Incidentally I am working on the AffyMetrix 500k chip as well
(http://www.wtccc.org.uk/) but I have already written a non-R C/C++
tool to dump all the probe signal of a whole array as an image
(not intended for html, obviously, for 6.5 million probes); and
another one for drawing the schematics of the locations of
probes associated with a specific snp as a postscript vector diagram.
I will probably be working on combining the two - i.e. overlaying
an image with a vector diagram next week. (which means I hope to get
an image of intensities with some cicles on top, highlighting the
effect on the intensities to a specific snp due to blemishes).

Hin-Tak Leung

Henrik Bengtsson wrote:
> Hi,
> 
> I try to create PNG images of a certain size where each pixel
> intensity corresponds to exactly one probe signal in an Affymetrix
> array.  I try to use png() and image() with zero margins to do this.
> Example:
> 
> z <- matrix(1:15, nrow=45, ncol=30)
> png("large.png", height=nrow(z), width=ncol(z), bg="red")
> par(mar=c(0,0,0,0))
> image(z, col=gray.colors(16), axes=FALSE)
> dev.off()
> 
> z <- matrix(1:15, nrow=5, ncol=3)
> png("tiny.png", height=nrow(z), width=ncol(z), bg="red")
> par(mar=c(0,0,0,0))
> image(z, col=gray.colors(16), axes=FALSE)
> dev.off()
> 
> The problem is that on WinXP the very bottom row and the very right
> column of pixels in red.  Trying on Linux, it is only the very right
> column that is red.  See attached images (you might have to zoom in to
> see it).  I try to do this in R v2.3.1.  The same effect is seen if
> the jpeg() device is used.
> 
> When rescaling, the same effect is seen (the red border effect is one
> pixel wide), e.g.
> 
> z <- matrix(1:15, nrow=45, ncol=30)
> png("large5.png", height=5*nrow(z), width=5*ncol(z), bg="red")
> par(mar=c(0,0,0,0))
> image(z, col=gray.colors(16), axes=FALSE)
> dev.off()
> 
> I might be asking for something that is not supported, but is there a
> way around this?  It is a problem, because I wish to tile the images
> in an HTML page.
> 
> Thanks
> 
> Henrik
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] png() and image()
Hin-Tak Leung