While using result.linkage.dendrogram_col or result.linkage.dendrogram_row will currently work, it seems to be an implementation detail. The safest route is to first compute the linkages explicitly and pass them to the clustermap function, which has row_linkage and col_linkage parameters just for that. Replacing the last line in your example (result = …) with the following code … Read more
There are three steps in hierarchical agglomerative clustering (HAC): Quantify Data (metric argument) Cluster Data (method argument) Choose the number of clusters Doing z = linkage(a) will accomplish the first two steps. Since you did not specify any parameters it uses the standard values metric=”euclidean” method = ‘single’ So z = linkage(a) will give you … Read more
It seems that indeed we cannot directly pass the redundant square matrix in, although the documentation claims we can do so. To benefit anyone who faces the same problem in the future, I write my solution as an additional answer here. So the copy-and-paste guys can just proceed with the clustering. Use the following snippet … Read more