setwd("[% TEMPDIR %]")

user <- read.delim("[% DATA %]", sep="\t", header=FALSE)

#
# Got this from
# https://stat.ethz.ch/pipermail/bioconductor/2003-October/002874.html
#
na.dist <- function(x,...) {
 t.dist <- dist(x,...)
 t.dist <- as.matrix(t.dist)
 t.limit <- 1.1*max(t.dist,na.rm=T)
 t.dist[is.na(t.dist)] <- t.limit
 t.dist <- as.dist(t.dist)
 return(t.dist)
}

label     <- user[,1]
selection <- as.matrix(user[,-1])

gene_distances                <- na.dist( selection )
attr(gene_distances,"Labels") <- label

gene_dendro <- hclust(gene_distances)

dimnames(selection)[[1]] <- user[,1]

dimnames(selection)[[2]] <- 1:length(selection[1,])


postscript(file= "[% HEATMAP %]", width=9, height=9, paper="special", horizontal=FALSE)

# See 
# https://stat.ethz.ch/pipermail/bioconductor/2003-November/003144.html
# for the coercion

heatmap(selection,Rowv=as.dendrogram(gene_dendro))

postscript(file= "[% DENDROGRAM %]", width=9, height=9, paper="special", horizontal=FALSE)

plot(gene_dendro)