Thanks James and Martin for your advice.

Martin, on my linux box the command 'gs -h' lists the available ghostscript devices etc. However I only know that because you pointed me to the right information ;-)

Thanks again

Iain

IAIN GALLAGHER <iaingallagher@btopenworld.com> 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.

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.

Could someone give me some guidance please?

Thanks

Iain

 [[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


	[[alternative HTML version deleted]]

