Emmanuel Paradis, the maintainer of the ape package was very helpful
in solving this problem. It seems that it heatmap does not reorder
the rows, so you must reorder them or change the heatmap code to do
so. The heatmap maintainers will document this, but not change the
behavior. The following
I am having trouble displaying a dendrogram of evolutionary
relationships (a phylogram imported from the ape package) as the
vertical component of a heatmap, but keeping the hierarchical
clustering of the horizontal component. The relationships of the
vertical component in the generated heatmap
