HclustParam-class {bluster} | R Documentation

## Hierarchical clustering

### Description

Run the base `hclust` function on a distance matrix within `clusterRows`.

### Usage

    HclustParam(
      metric = NULL,
      method = NULL,
      cut.fun = NULL,
      cut.dynamic = FALSE,
      cut.height = NULL,
      cut.number = NULL,
      cut.params = list(),
      ...
    )

    ## S4 method for signature 'ANY,HclustParam'
    clusterRows(x, BLUSPARAM, full = FALSE)

### Arguments

`metric` | String specifying the distance metric to use in `dist`.
`method` | String specifying the agglomeration method to use in `hclust`.
`cut.fun` | Function specifying the method to use to cut the dendrogram. The first argument of this function should be the output of `hclust`, and the return value should be an atomic vector specifying the cluster assignment for each observation. Defaults to `cutree` if `cut.dynamic=FALSE` and `cutreeDynamic` otherwise.
`cut.dynamic` | Logical scalar indicating whether a dynamic tree cut should be performed using the dynamicTreeCut package.
`cut.height, cut.number` | Deprecated, use `h` and `k` in `cut.params` instead.
`cut.params` | Further arguments to pass to `cut.fun`.
`...` | Deprecated, more arguments to add to `cut.params`.
`x` | A numeric matrix-like object where rows represent observations and columns represent variables.
`BLUSPARAM` | A HclustParam object.
`full` | Logical scalar indicating whether the hierarchical clustering statistics should be returned.

### Details

To modify an existing HclustParam object `x`, users can simply call `x[[i]]` or `x[[i]] <- value` where `i` is any argument used in the constructor.

If `cut.fun=NULL`, `cut.dynamic=FALSE` and `cut.params` does not have `h` or `k`, `clusterRows` will automatically set `h` to half the tree height when calling `cutree`.

### Value

The `HclustParam` constructor will return a HclustParam object with the specified parameters.

The `clusterRows` method will return a factor of length equal to `nrow(x)` containing the cluster assignments. If `full=TRUE`, a list is returned with `clusters` (the factor, as above) and `objects` (a list containing `dist`, the distance matrix; and `hclust`, the output of `hclust`).

### Author(s)

Aaron Lun

### See Also

`dist`, `hclust` and `cutree`, which actually do all the heavy lifting.

`cutreeDynamic`, for an alternative tree cutting method to use in `cut.fun`.

### Examples

    clusterRows(iris[,1:4], HclustParam())
    clusterRows(iris[,1:4], HclustParam(method="ward.D2"))

[Package bluster version 1.2.1 Index]