epurdom
makeDendrogram order samples within a cluster
makeDendrogram should somehow order the samples within a cluster, if it doesn't already. I.e. cluster within each cluster and make that the order, even if dendrogram doesn't change.
This could probably be done by getting the order within each cluster via hclust within cluster, then concatenating the orders to get a single ordering and using the reorder.dendrogram function on the current dendrogram.
The order idea doesn't work. At least not well, because only will rotate existing left/right. Have to create method to paste the trees together. Much more annoying... Have started some code with ape package, but very frustrating.
Also, now the internal code relies heavily on 0-length edges within a cluster to distinguish cluster nodes and outbranch nodes ... so must be careful not to disrupt that.