png() and image()

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

Hi Henrik,
this does not directly answer your question, but you might be able to
use the function write.image in the package EBImage (Bioconductor) to
write matrices into image files (e.g. PNG or JPEG), this might be more
flexible and also faster than what you're trying to do.
  Best wishes
  Wolfgang
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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

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

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Hi Wolfgang,

thanks for this - I took a look the EBImage webpage
[http://www.ebi.ac.uk/~osklyar/projects/EBImage/] and it looks very
nice.  Are there any plans for Windows support too?  I am looking for
a cross-platform solution.

Cheers

On 7/21/06, Wolfgang Huber <huber at ebi.ac.uk> wrote:

Hi Henrik,
this does not directly answer your question, but you might be able to
use the function write.image in the package EBImage (Bioconductor) to
write matrices into image files (e.g. PNG or JPEG), this might be more
flexible and also faster than what you're trying to do.
  Best wishes
  Wolfgang
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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

Henrik Bengtsson wrote:

Hi Wolfgang,

thanks for this - I took a look the EBImage webpage
[http://www.ebi.ac.uk/~osklyar/projects/EBImage/] and it looks very
nice.  Are there any plans for Windows support too?  I am looking for
a cross-platform solution.

Cheers

Hi Henrik,

there are very strong intentions to also make this available as a
Windows precompiled package and/or provide installation instruction for
Windows. Until now however, in spite of some effort, we have failed.

As I understand it, a problem seems to be different dll formats of  MS
Visual C++ (in which ImageMagick is provided) and MinGW.

If anyone is interested in helping with this, they could have a look at
the source package on Bioconductor, and contact us for details.

 Best wishes
 Wolfgang

On 7/21/06, Wolfgang Huber <huber at ebi.ac.uk> wrote:

Hi Henrik,
this does not directly answer your question, but you might be able to
use the function write.image in the package EBImage (Bioconductor) to
write matrices into image files (e.g. PNG or JPEG), this might be more
flexible and also faster than what you're trying to do.
  Best wishes
  Wolfgang
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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

Wolfgang Huber wrote:

Henrik Bengtsson wrote:

Hi Wolfgang,

thanks for this - I took a look the EBImage webpage
[http://www.ebi.ac.uk/~osklyar/projects/EBImage/] and it looks very
nice.  Are there any plans for Windows support too?  I am looking for
a cross-platform solution.

Cheers

Hi Henrik,

there are very strong intentions to also make this available as a
Windows precompiled package and/or provide installation instruction for
Windows. Until now however, in spite of some effort, we have failed.

As I understand it, a problem seems to be different dll formats of  MS
Visual C++ (in which ImageMagick is provided) and MinGW.

If anyone is interested in helping with this, they could have a look at
the source package on Bioconductor, and contact us for details.

It is probably easier to port ImageMagick to MinGW than to try to
link mingw-compiled EBImage against MSVC++ compiled imagemagick.

(Imagemagick does run under cygwin, I believe, so it is not
entirely hostile to gcc on windows).

HTL

 Best wishes
 Wolfgang

On 7/21/06, Wolfgang Huber <huber at ebi.ac.uk> wrote:

Hi Henrik,
this does not directly answer your question, but you might be able to
use the function write.image in the package EBImage (Bioconductor) to
write matrices into image files (e.g. PNG or JPEG), this might be more
flexible and also faster than what you're trying to do.
  Best wishes
  Wolfgang
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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