Dear All: I tried to use heatmap.2 to generate hierarchical clustering using the following command: heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) datamatrix is subset of a RMA normalized data subset by a genelist. The problem is a lot of times, the z-score in key are from, like -5 to 15 or -15 to 5, as a result, the zero of z distribution are are either green region or red region of the key, the resulting heatmap are either generally greenish or redish. I wonder if there is a way to make the heatmap more balanced between red and green, I tried to read the heatmap.2 help but could not get a clear idea. Thanks Hao [[alternative HTML version deleted]]
the heatmapCol function of package MKmisc might help ... try: library(MKmisc) example("heatmapCol") Best Matthias Liu, Hao [CNTUS] wrote:> Dear All: > > I tried to use heatmap.2 to generate hierarchical clustering using the following command: > > heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) > > datamatrix is subset of a RMA normalized data subset by a genelist. > > The problem is a lot of times, the z-score in key are from, like -5 to 15 or -15 to 5, as a result, the zero of z distribution are are either green region or red region of > the key, the resulting heatmap are either generally greenish or redish. > > I wonder if there is a way to make the heatmap more balanced between red and green, I tried to read the heatmap.2 help but could not get a clear idea. > > Thanks > Hao > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Dr. Matthias Kohl stamats.de