[BioC] heatmap.2

Kauer Maximilian Otto maximilian.kauer at ccri.at
Tue Dec 23 16:07:43 CET 2008

You can use the heatmapCol function from the Slmisc package

Maximilian Kauer
CCRI - Children's Cancer Research Institute

-----Ursprüngliche 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?

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.

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