I would leave my table as a heatmap where darker colors represent higher similarity, and the lighter colors represent less level of similarity. I'm using version 2.11 of R.
I once used this code, maybe it will help you: #dendogram plot(dendro15, labels = cellType) ### I first made a dendrogram of my data #heatmap specifications # Filter genes on variance otherwise the heatmap cannot be shown. em <- exprs(ALL)[which(apply(exprs(ALL), 1, sd) > 1.75), ] #### I had so many genes I had to filter them pal <- maPalette(low="blue", high="yellow", mid=NULL, k=25) #### You can make a color palet here to specify ## the light and dark colors. ### Heatmap heatmap(em, Colv=as.dendrogram(dendro15), col=pal, labCol=cellType) -- View this message in context: http://r.789695.n4.nabble.com/Matrix-heatmap-tp4619084p4619683.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.