[BioC] Heatmap: row labels & dendogram

Saroj K Mohapatra saroj at vt.edu
Wed Mar 24 18:23:24 CET 2010

Hi Daniela:

danieladna wrote:
> Hi,
> A two questions about heatmap.2 :
> What is the best approach to make the row labels readable? 
> Right now they are merging. I plotted 104 genes. The command cexRow
> is not giving me the desired result, since the font size 
> needs to be set extremly small to fit all in;
> so small that no one can read it!!!
What if you write the output to a file?
# Create some data with 104 rows
mydat=matrix(rnorm(1040), nrow=104)

# start graphics device driver; write to PDF
pdf(file="temp.pdf", height=20) # note the height parameter

# Heatmap with no dendrogram, no left top key, no trace
heatmap.2(mydat, dendrogram="none", mar=c(2,2), key=F, keysize=0.1, 

# shut down the graphics device

Now the temp.pdf file should have the row names visible. You may want to 
play with the 'height' parameter for improving.

> How can I switch off the dendogram drawing option? I like the dendogram
> to be computed and reordered based on row means, but I do not like it
> to be displayed!
as in the example above.


> Many thanks for your help,
> Daniela
> 	[[alternative HTML version deleted]]
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