[BioC] heatmap.2 how to remove row separator

[Wolfgang Huber]

Just for completeness, a small addition to the code example below: 
either the argument to the level.plot function should be 
'col.regions=col', or it can be just omitted. This does not change any 
of the reasoning about little white lines or file sizes.

	Wolfgang

Wolfgang Huber scripsit 25/02/11 16:11:
> Dear Benoit
>
> in my experience this depends on the PDF viewer. For me, your PDF file
> http://tinyurl.com/6yqcswr shows a hint of those white lines in
> "Document Viewer 2.32.0", while it does not on "Adobe Reader 9.4.1"
> (both on Ubuntu).
>
> R's image function, on which these plots are based, is pretty peculiar -
> it draws each matrix element as a filled polygon. Recently, support for
> raster images was added to R devices, and this might be an alternative.
> E.g., for the case of levelplot:
>
>
> library("lattice")
>
> m = matrix(runif(10000), nrow=5)
> m[3,] = 0
>
> col = heat.colors(100)
>
> pdf("tmp1.pdf", width=5, height=10)
> print(levelplot(m, col=col, aspect="fill"))
> dev.off()
>
> pdf("tmp2.pdf", width=5, height=10)
> print(levelplot(m, col=col, aspect="fill",panel= panel.levelplot.raster))
> dev.off()
>
>
> tmp1.pdf has 594 kB and shows the white stripes in Document Viewer,
> while tmp2.pdf has 73 kB and does not show white stripes.
>
> Best wishes
> Wolfgang
>
> Benoît Ballester scripsit 23/02/11 16:33:
>> Hi James,
>>
>> James W. MacDonald wrote:
>>
>>> Then zoom in on the resulting pdf. There will be some small white
>>> lines, but IMO they are very unobtrusive.
>>
>> Indeed this is exactly what I see, and I do find it annoying. Have a
>> look at the links below. You'll notice the difference between PDF (with
>> white lines) and PNG (I believe without)
>>
>>
>> http://tinyurl.com/6yqcswr
>> http://tinyurl.com/67wkbl3
>>
>>
>>
>>> Your other choice is to use levelplot() from lattice, but you will
>>> still get white lines:
>>>
>>> library(lattice)
>>> pdf("tmp2.pdf", width=5, height=50)
>>> levelplot(matrix(rnorm(10000), nrow=10), col=redgreen(100),
>>> colorkey=FALSE)
>>> dev.off()
>>>
>>
>> This seems to work slightly better.
>> I'll give it a try...
>>
>> Ben
>>
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>
>


-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber