Dear Bioconductors, i have a question about parameters of heatmap.2 function in gplots. I am plotting log10 pvalues ranging from say -40 to 20 using a redblue and want to produce a key which reflects this distribution: Negative pvalues in blue, positive in red. as the distribution is not symmetric, there seems to be a problem. The symkey parameter, if set in TRUE, makes the color key symmetric about 0). I want to assign more blue colors of the panel to negative pvalues and less colors of the red panel in positive, but I realize this is not what symkey does: the key layout is centred around zero, but the color distribution not: white (middle panel) colors are around -10, whereas after +10 the key colors are just absent Here are my parameters: heatmap.2(tabNew, Rowv=as.dendrogram(hrR), Colv=as.dendrogram(hrC), col=redblue(100)[100:1], scale="none", key=TRUE, keysize=0.7, symkey=TRUE, trace="none", cexRow=0.8, cexCol=1.1, margins=c(8,32), main=paste(name, '_', dim(tabNew)[1], ' categories', sep='') ) I work with R.2.6 version. How can I achieve this? I do not want to change my values and make them symmetric, as I d like toi reflect the unequal distribution. Any ideas? Thanks, Natassa Gioti Research Associate - Bioinformatics Institute of Healthy Ageing, and GEE Room 326, The Darwin Building University College London Gower Street, London WC1E 6BT, UK.

On Tue, Dec 23, 2008 at 9:19 AM, Anastasia Gioti <a.gioti@ucl.ac.uk> wrote: > > Dear Bioconductors, > i have a question about parameters of heatmap.2 function in gplots. I am > plotting log10 pvalues ranging from say -40 to 20 using a redblue and want > to produce a key which reflects this distribution: Negative pvalues in > blue, positive in red. as the distribution is not symmetric, there seems > to be a problem. The symkey parameter, if set in TRUE, makes the color key > symmetric about 0). I want to assign more blue colors of the panel to > negative pvalues and less colors of the red panel in positive, but I > realize this is not what symkey does: the key layout is centred around > zero, but the color distribution not: white (middle panel) colors are > around -10, whereas after +10 the key colors are just absent > Here are my parameters: > heatmap.2(tabNew, Rowv=as.dendrogram(hrR), Colv=as.dendrogram(hrC), > col=redblue(100)[100:1], scale="none", key=TRUE, keysize=0.7, symkey=TRUE, > trace="none", cexRow=0.8, cexCol=1.1, margins=c(8,32), main=paste(name, > '_', dim(tabNew)[1], ' categories', sep='') ) > I work with R.2.6 version. > > How can I achieve this? I do not want to change my values and make them > symmetric, as I d like toi reflect the unequal distribution. Any ideas? > You'll want to play with the breaks argument. See the help for more details. Hope that gets you going. Sean [[alternative HTML version deleted]]

On Tue, Dec 23, 2008 at 10:19 AM, Anastasia Gioti <a.gioti@ucl.ac.uk> wrote: > > > Dear Sean, > > Thanks for help. I followed your advise and with breaks=seq(-3,3,0.05997), > which gives a vector of 101, I can plot my 100 colors of the redblue > panel. However, now i loose the coloring gradient, everything is either > dark blue/ > dark red. You told heatmap.2 to use colors from -3 to 3. I think you mentioned that your data go from -40 to 20? Perhaps you could use that range instead of -3 to 3? Sean [[alternative HTML version deleted]]

You can use the heatmapCol function from the Slmisc package max -------------------------------------- Maximilian Kauer CCRI - Children's Cancer Research Institute -----Urspr?ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch im Auftrag von Anastasia Gioti Gesendet: Di 23.12.2008 15:19 An: bioconductor at stat.math.ethz.ch Betreff: [BioC] heatmap.2 Dear Bioconductors, i have a question about parameters of heatmap.2 function in gplots. I am plotting log10 pvalues ranging from say -40 to 20 using a redblue and want to produce a key which reflects this distribution: Negative pvalues in blue, positive in red. as the distribution is not symmetric, there seems to be a problem. The symkey parameter, if set in TRUE, makes the color key symmetric about 0). I want to assign more blue colors of the panel to negative pvalues and less colors of the red panel in positive, but I realize this is not what symkey does: the key layout is centred around zero, but the color distribution not: white (middle panel) colors are around -10, whereas after +10 the key colors are just absent Here are my parameters: heatmap.2(tabNew, Rowv=as.dendrogram(hrR), Colv=as.dendrogram(hrC), col=redblue(100)[100:1], scale="none", key=TRUE, keysize=0.7, symkey=TRUE, trace="none", cexRow=0.8, cexCol=1.1, margins=c(8,32), main=paste(name, '_', dim(tabNew)[1], ' categories', sep='') ) I work with R.2.6 version. How can I achieve this? I do not want to change my values and make them symmetric, as I d like toi reflect the unequal distribution. Any ideas? Thanks, Natassa Gioti Research Associate - Bioinformatics Institute of Healthy Ageing, and GEE Room 326, The Darwin Building University College London Gower Street, London WC1E 6BT, UK. _______________________________________________ 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