Need to reconcile clustering functionalities

[jamesmkrieger]

We currently have quite a few of these and it's not clear what the differences between them are. These include:

• The kwarg cluster_col in showPerturbResponse, which does nothing except affect the xlabel
• The kwarg cluster in showAtomicMatrix, which likewise does nothing
• The function clusterMatrix in utilities/catchall.py, which reorders a matrix using scipy.cluster.hierarchy
• The function reorderMatrix in utilities/catchall.py, which reorders a matrix using a precalculated tree
• The function findSubgroups in utilities/catchall.py, which finds subgroups from a tree and optionally uses scipy.cluster.hierarchy.fcluster on a linkage matrix
• The incoming function clusterSubfamilies in pull request Added calcModeClusters method to utilities/catchall.py #1098

There are probably more too. For example, the function calcTree likely has some other redundant relatives.

[jamesmkrieger]

Now we also have calcGromosClusters in #1406