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]]

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 > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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

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]]