Self-organizing map (SOM) example in R

SOM example.R

#SOM example using wines data set
library(kohonen)
data(wines)
set.seed(7)

#create SOM grid
sommap <- som(scale(wines), grid = somgrid(2, 2, "hexagonal"))

## use hierarchical clustering to cluster the codebook vectors
groups<-3
som.hc <- cutree(hclust(dist(sommap$codes)), groups)

#plot
plot(sommap, type="codes", bgcol=rainbow(groups)[som.hc])

#cluster boundaries
add.cluster.boundaries(sommap, som.hc)

following works

som.hc <- cutree(hclust(dist(sommap$codes[[1]])), groups)

I follow yours suggested and it works

related blog post: https://imdevsoftware.wordpress.com/2016/05/19/push-it-to-the-limit-som-clustering-networks/