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Question: Heatmap: row labels & dendogram
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gravatar for danieladna
7.7 years ago by
danieladna110
danieladna110 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!!! 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! Many thanks for your help, Daniela [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.7 years ago by Saroj K Mohapatra390 • written 7.7 years ago by danieladna110
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gravatar for Saroj K Mohapatra
7.7 years ago by
Saroj K Mohapatra390 wrote:
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, trace="none") # shut down the graphics device dev.off() 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! > > dendrogram="none" as in the example above. Best, Saroj > Many thanks for your help, > Daniela > > > > > [[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 > >
ADD COMMENTlink written 7.7 years ago by Saroj K Mohapatra390
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