## 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)
## run affinity propagation using negative squared Euclidean
apres <- apcluster(negDistMat(r=2), x, p=-0.1)
## plot heatmap clustering run
heatmap(apres)
## rerun affinity propagation
## reuse similarity matrix from previous run
apres2 <- apcluster(s=apres@sim, q=0.6)
## plot heatmap of second run
heatmap(apres2, apres@sim)
## with alternate heatmap coloring, alternating color bars, and no dendrograms
heatmap(apres2, apres@sim, Rowv=NA, Colv=NA,
sideColors=c("darkgreen", "yellowgreen"), col=terrain.colors(12))
## perform agglomerative clustering of affinity propagation clusters
aggres1 <- aggExCluster(apres@sim, apres2)
## plot heatmap
heatmap(cutree(aggres1, 2), apres@sim)
## perform agglomerative clustering of whole data set
aggres2 <- aggExCluster(negDistMat(r=2), x)
## show heatmap along with dendrogram
heatmap(aggres2)
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