Very nice, thank you James and Sean. -levi On Fri, May 1, 2009 at 2:28 PM, James F. Reid <james.reid@ifom-ieo- campus.it=""> wrote: > Hi Levi, > > maybe Heatplus is what you are looking for: > <http: www.bioconductor.org="" packages="" release="" bioc="" html="" heatplus.html=""> > > HTH. > J. > > > Levi Waldron wrote: > >> Can someone recommend a more sophisticated way to annotate heatmaps than >> the >> ColSideColors argument of heatmap and heatmap.2? In particular, I would >> like to be able to annotate columns with more than one piece of >> information, >> like in Figure 1 of the article at >> http://www3.interscience.wiley.com/cgi- bin/fulltext/117905619/HTMLSTART / >> doi:10.1002/hep.22256. >> >> Some example data and a heatmap: >> >> set.seed(1) >> y <- matrix(rnorm(100),nrow=20,ncol=5) >> colnames(x) <- LETTERS[1:5] >> rownames(x) <- paste("r",1:20,sep="") >> set.seed(1) >> annotation <- matrix(sample(c("+","-"),15,replace=TRUE),ncol=5) >> colnames(annotation) <- colnames(x) >> rownames(annotation) <- paste("annotation",1:3) >> >> heatmap(x,Rowv=NA, >> ColSideColors=sapply(annotation[1,],function(x) >> switch(x,"+"="red","-"="blue"))) >> >> This heatmap annotates the columns by the first of the three annotations >> with a colored bar along the top of the heatmap, but ideally I would like >> to >> put all three annotations on the heatmap by putting three rows of +/- >> symbols between the top of the heatmap and the dendrogram, or >> alternatively >> three colored bars. Specific or general suggestions would be welcome. >> >> Thank you, >> Levi >> >> -- Levi Waldron post-doctoral fellow Jurisica Lab, Ontario Cancer Institute Division of Signaling Biology IBM Life Sciences Discovery Centre TMDT 9-304D 101 College Street Toronto, Ontario M5G 1L7 (416)581-7453 [[alternative HTML version deleted]]