[BioC] heatmap.2 how to remove row separator

[James W. MacDonald]

Hi Ben,

On 2/23/2011 8:20 AM, Benoît Ballester wrote:
> Hi,
>
> I am trying to plot a heatmap with heatmap.2, and would like not to plot
> any block separation for all rows, which is "white" by default.

The default is to not draw separators. There will be some very thin 
white lines between the rows and columns, but this is due to how image() 
works (and in the end, heatmap.2 relies on image() to create the 
heatmap). For instance, try

library(gplots)
pdf("tmp.pdf", width=5, height=50)
image(1:10, 1:1000, matrix(rnorm(10000), nrow=10), col=redgreen(25))
dev.off()

Then zoom in on the resulting pdf. There will be some small white lines, 
but IMO they are very unobtrusive.

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()


Best,

Jim



>
> When I plot my heatmap as PDF (~9000 rows) I get all those fin white
> lines which dilutes the colors in my heatmap. A bit blurry in a way.
>
> I have played with those parameters, but with no luck so far.
>
> # block sepration
> colsep,
> rowsep,
> sepcolor="white",
> sepwidth=c(0.05,0.05),
>
> If any of you have an idea, or know how to deal with this, I'll be more
> than happy to hear about it.
>
> Thanks,
>
> Ben
>
> ( R-2.12.0 )
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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