I am running hierarchical clustering with a distance matrix M_norm:
hc <- hclust(M_norm^2, method="ward.D")
plot(hc, cex=1, hang=-1)
When I use different
M_norm, the resulting dendrogram changes a little bit: heights where certain branches are joined are not the same as before. The height of the final join is also different.
The order of rows and columns in the input matrix is now different, but the distances between units are the same. I understand that the order of units at the bottom of the picture can change, but how can this happen? Is the implementation of this algorithm not deterministic?