apcluster (version 1.2.1)

AggExResult-class: Class "AggExResult"

Description

S4 class for storing results of exemplar-based agglomerative clustering

Objects

Objects of this class can be created by calling aggExCluster for a given similarity matrix.

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: http://dx.doi.org/10.1093/bioinformatics/btr406{10.1093/bioinformatics/btr406}.

See Also

aggExCluster, show-methods, plot-methods, cutree-methods

Examples

## create two Gaussian clouds
cl1 <- cbind(rnorm(50,0.2,0.05),rnorm(50,0.8,0.06))
cl2 <- cbind(rnorm(50,0.7,0.08),rnorm(50,0.3,0.05))
x <- rbind(cl1,cl2)

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

## compute agglomerative clustering from scratch
aggres1 <- aggExCluster(sim)

## show results
show(aggres1)

## plot dendrogram
plot(aggres1)

## plot heatmap along with dendrogram
plot(aggres1, sim)

## plot level with two clusters
plot(aggres1, x, k=2)

## run affinity propagation
apres <- apcluster(sim, q=0.7)

## create hierarchy of clusters determined by affinity propagation
aggres2 <- aggExCluster(sim, apres)

## show results
show(aggres2)

## plot dendrogram
plot(aggres2)

## plot heatmap
plot(aggres2, sim)

## plot level with two clusters
plot(aggres2, x, k=2)