Dear all I use heatmap.2 to generate a heatmap, but the generated pdf seems very cloudy !!! I use the following lines of code, can anyone help allocate where the problem is ?? # generate heatmap for matrix bb hc <- hclust(as.dist(1-cor(as.matrix(bb), method="spearman")), method="complete", members=NULL) # Clusters columns by Spearman correlation as distance method. hr <- hclust(as.dist(1-cor(t(as.matrix(bb)), method="spearman")), method="complete", members=NULL) mycl <- cutree(hr, h=max(hr$height)/1.5); mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9); mycolhc <- mycolhc[as.vector(mycl)] # Cuts the tree and creates color vector for clusters. library(gplots); myheatcol <- redgreen(75) pdf("heatmap_dataset1.pdf") heatmap.2(bb, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), col=myheatcol, scale="row", density.info="none", trace="none", RowSideColors=mycolhc) dev.off() Thanks a lot yours, Alyaa -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]

I don't quite get what kind of cloudness Alyaa have. If it is about margin. the parameters margin, lhei might help. Wenhuo On Apr 11, 2012 8:40 AM, "Alyaa Mahmoud" <alyamahmoud@gmail.com> wrote: > Dear all > > I use heatmap.2 to generate a heatmap, but the generated pdf seems very > cloudy !!! I use the following lines of code, > can anyone help allocate where the problem is ?? > > # generate heatmap for matrix bb > hc <- hclust(as.dist(1-cor(as.matrix(bb), method="spearman")), > method="complete", members=NULL) > # Clusters columns by Spearman correlation as distance method. > hr <- hclust(as.dist(1-cor(t(as.matrix(bb)), method="spearman")), > method="complete", members=NULL) > > mycl <- cutree(hr, h=max(hr$height)/1.5); > mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9); > mycolhc <- mycolhc[as.vector(mycl)] # Cuts the tree and creates color > vector for clusters. > > library(gplots); > myheatcol <- redgreen(75) > pdf("heatmap_dataset1.pdf") > heatmap.2(bb, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), > col=myheatcol, scale="row", density.info="none", trace="none", > RowSideColors=mycolhc) > dev.off() > > > Thanks a lot > yours, > Alyaa > > -- > Alyaa Mahmoud > > "Love all, trust a few, do wrong to none"- Shakespeare > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]