How to draw a heatmap in R using heatmap.3 package

Question

I've seen a few sources to draw a heatmap in R using the standard heatmap and heatmap.2 packages, but I have yet to come across an example using the new heatmap.3 package. The only source I could find for this was https://www.biostars.org/p/18211/. However, even here, the author makes his own heatmap.3 package, not the standard heatmap.3 package from CRAN http://cran.r-project.org/web/packages/GMD/GMD.pdf. I tried figuring out how to make a heatmap with heatmap.3 from that CRAN documentation, but I didn't even know where to start. I immediately got lost in all the 50+ options. Can anyone get me started?

My tab-delimited input file looks like this:

EntryA  EntryB  EntryC  EntryD  EntryE
John    48  31  57  55
Mary    88  11  89  78
Sarah   33  66  42  54

Answer 1

See below a basic example using heatmap 3 on your data (for a nicer plot, axes etc need to be edited). The critical step is to create a matrix with rownames. I turned the data.frame to a matrix as this is done in the examples provided in the GMD manual but it also works fine on data.frames.

library(GMD)

dat<-data.frame(EntryA=as.numeric(c(48,88,33)), EntryB=as.numeric(c(31,11,66)), EntryC=as.numeric(c(57,89,42)), EntryD=as.numeric(c(55,78,54)))

rownames(dat)=c("John","Mary","Sarah") 

ndat<-as.matrix(dat)

heatmap.3(ndat, Rowv=FALSE, Colv=FALSE)