R - silhouette with observation labels
I am doing hierarchical clustering with batch cluster
in R. Using a function silhouette
, I can get a silhouette plot to output my cluster for any given height (h) in the dendrogram.
# run hierarchical clustering
if(!require("cluster")) { install.packages("cluster"); require("cluster") }
tmp <- matrix(c( 0, 20, 20, 20, 40, 60, 60, 60, 100, 120, 120, 120,
20, 0, 30, 50, 60, 80, 40, 80, 120, 100, 140, 120,
20, 30, 0, 40, 60, 80, 80, 80, 120, 140, 140, 80,
20, 50, 40, 0, 60, 80, 80, 80, 120, 140, 140, 140,
40, 60, 60, 60, 0, 20, 20, 20, 60, 80, 80, 80,
60, 80, 80, 80, 20, 0, 20, 20, 40, 60, 60, 60,
60, 40, 80, 80, 20, 20, 0, 20, 60, 80, 80, 80,
60, 80, 80, 80, 20, 20, 20, 0, 60, 80, 80, 80,
100, 120, 120, 120, 60, 40, 60, 60, 0, 20, 20, 20,
120, 100, 140, 140, 80, 60, 80, 80, 20, 0, 20, 20,
120, 140, 140, 140, 80, 60, 80, 80, 20, 20, 0, 20,
120, 120, 80, 140, 80, 60, 80, 80, 20, 20, 20, 0),
nr=12, dimnames=list(LETTERS[1:12], LETTERS[1:12]))
cl <- hclust(as.dist(tmp,diag = TRUE, upper = TRUE), method= 'single')
sil_cl <- silhouette(cutree(cl, h=25) ,as.dist(tmp), title=title(main = 'Good'))
plot(sil_cl)
This gives the figure below and this is what disappoints me. How can I use watch labels rownames(tmp)
in the silhouette plot rather than numeric indices (1 to 12), which doesn't make any sense to me.
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1 answer
I'm not sure why, but the call silhouette
seems to leave the row names. You can add them back with
cl <- hclust(as.dist(tmp,diag = TRUE, upper = TRUE), method= 'single')
sil_cl <- silhouette(cutree(cl, h=25) ,as.dist(tmp), title=title(main = 'Good'))
rownames(sil_cl) <- rownames(tmp)
plot(sil_cl)
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