I give an answer here, that indirectly answers your question: A: Heatmap based with FPKM values

In a nutshell, just add the following as parameters to heatmap.2():

#Euclidean distance with Ward's linkage
heatmap.2(
  ...,
  distfun = function(x) dist(x, method="euclidean"),
  hclustfun = function(x) hclust(x, method="ward.D2"))

#1 minus Pearson correlation distance with average linkage
heatmap.2(
  ...,
  distfun = function(x) as.dist(1-cor(t(x))),
  hclustfun = function(x) hclust(x, method="average"))

et cetera