R: Class "ExClust"

ExClust-class {apcluster} | R Documentation

## Class "ExClust"

### Description

S4 class for storing exemplar-based clusterings

### Objects

Objects of this class can be created by calling `cutree` to cut out a clustering level from a cluster hierarchy of class `AggExResult`. Moreover, `cutree` can also be used to convert an object of class `APResult` to class `ExClust`.

### Slots

The following slots are defined for ExClust objects:

`l`:

  number of samples in the data set

`sel`:

  subset of samples used for leveraged clustering

`exemplars`:

  vector containing indices of exemplars

`clusters`:

  list containing the clusters; the i-th component is a vector of indices of data points belonging to the i-th exemplar (including the exemplar itself)

`idx`:

  vector of length `l` realizing a sample-to-exemplar mapping; the i-th entry contains the index of the exemplar the i-th sample belongs to

`sim`:

  similarity matrix; only available if the preceding clustering method was called with `includeSim=TRUE`.

`call`:

  method call of the preceding clustering method

### Methods

plot

  `signature(x="ExClust")`: see `plot-methods`

plot

  `signature(x="ExClust", y="matrix")`: see `plot-methods`

heatmap

  `signature(x="ExClust")`: see `heatmap-methods`

heatmap

  `signature(x="ExClust", y="matrix")`: see `heatmap-methods`

show

  `signature(object="ExClust")`: see `show-methods`

labels

  `signature(object="ExClust")`: see `labels-methods`

cutree

  `signature(object="ExClust", k="ANY", h="ANY")`: see `cutree-methods`

length

  `signature(x="ExClust")`: gives the number of clusters.

sort

  `signature(x="ExClust")`: see `sort-methods`

as.hclust

  `signature(x="ExClust")`: see `coerce-methods`

as.dendrogram

  `signature(object="ExClust")`: see `coerce-methods`

### Accessors

In the following code snippets, `x` is an `ExClust` object.

  `x[[i]]`: Returns the i-th cluster as a list of indices of samples belonging to the i-th cluster.

  `x[i]`: Returns a list of integer vectors with the indices of samples belonging to this cluster. The list has as many components as the argument `i` has elements. A list is returned even if `i` is a single integer.

similarity

  `signature(x="ExClust")`: gives the similarity matrix.

### Author(s)

Ulrich Bodenhofer, Andreas Kothmeier & Johannes Palme apcluster@bioinf.jku.at

### References

http://www.bioinf.jku.at/software/apcluster

Bodenhofer, U., Kothmeier, A., and Hochreiter, S. (2011) APCluster: an R package for affinity propagation clustering. Bioinformatics 27, 2463-2464. DOI: 10.1093/bioinformatics/btr406.

### See Also

`aggExCluster`, `show-methods`, `plot-methods`, `labels-methods`, `cutree-methods`, `AggExResult`, `APResult`

### Examples

    ## create two Gaussian clouds
    cl1 <- cbind(rnorm(20, 0.2, 0.05), rnorm(20, 0.8, 0.06))
    cl2 <- cbind(rnorm(25, 0.7, 0.08), rnorm(25, 0.3, 0.05))
    x <- rbind(cl1, cl2)

    ## compute similarity matrix (negative squared Euclidean)
    sim <- negDistMat(x, r=2)

    ## run affinity propagation
    aggres <- aggExCluster(sim)

    ## extract level with two clusters
    excl <- cutree(aggres, k=2)

    ## show details of clustering results
    show(excl)

    ## plot information about clustering run
    plot(excl, x)

[Package apcluster version 1.4.7 Index]