HierarchicalParam-class {bluster} | R Documentation

## The HierarchicalParam class

### Description

The HierarchicalParam is a virtual subclass of the BlusterParam class. It causes `clusterRows` to dispatch to clustering algorithms that produce a dissimilarity matrix and a dendrogram.

### Available slots

The virtual class provides `metric`, the choice of distance metric. This is conventionally passed to `dist` and defaults to a Euclidean distance in most subclasses.

It also provides a number of slots to manage the final tree cut:

- `cut.fun`, a function that takes a hclust object as its first argument and returns a vector of cluster assignments. If `NULL`, the choice of function is determined from `cut.dynamic`.

- `cut.dynamic`, a logical scalar indicating whether a dynamic tree cut should be performed by `cutreeDynamic`. Otherwise `cutree` is used. Ignored if `cut.fun` is not `NULL`.

- `cut.params`, further arguments to pass to the tree cut function specified by the previous arguments.

### Return value

The contract is that, when `full=TRUE`, the `objects` field of the `clusterRows` return value will always contain at least the following elements:

- `dist`, a dist object containing a dissimilarity matrix, usually a distance matrix.

- `hclust`, a hclust object containing a dendrogram.

### See Also

HclustParam, for the archetypal example of a concrete subclass.

[Package bluster version 1.4.0 Index]