[BioC] heatmap.2 tiff output help please

[James W. MacDonald]

Hi Iain,

IAIN GALLAGHER wrote:
> Hello list.
> 
> I am trying to draw a heatmap to publication standard. Currently I am
> having two problems.
> 
> The first is that when I try to output a tiff file with:
>> heatmap_data<-as.matrix(t(cropped_data)) 
>> heatcol<-colorRampPalette(brewer.pal(10, "RdBu"))(256) 
>> bitmap('cph_rma_ll_data_heatmap.tiff', type='tifflzw', res=600,
>> height=17.8, width=8.9, units='cm', pointsize=12) 
>> heatmap.2(heatmap_data, col=heatcol, main='RMA Data', key=F,
>> trace='none', labRow=labs, labCol=F, dendrogram='row') dev.off()
> 
> I am getting a grayscale image rather than a colour image. I presume
> that this is because of my misunderstanding RColorBrewer.

It's because you are using type="tifflzw". Remove that from your call to
bitmap and you get color.
> 
> The second problem relates to the layout in heatmap.2. Ideally, since
> I am not using the row dendrogram or the scale I would like my image
> to occupy a plotting space of one row and two columns (to contain the
> column dendrogram and the heatmap itself). However I cannot get the
> lmat, lhei and lwid parameters right to achieve this. The image
> should be 8.9cm wide which would occupy 1 column of the (hopeful)
> publishers figure layout.

Does adding

lmat = matrix(4:1, ncol = 2, byrow = TRUE), lhei = c(0.1,4)

to your call to heatmap.2 help?

Best,

Jim


> 
> Could someone give me some guidance please?
> 
> Thanks
> 
> Iain
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623