plot - R clustering- silhouette with observation labels -


i hierarchical clustering cluster package in r. using silhouette function, can silhouette plot of cluster output given height (h) cut-off in 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 figure below, point frustrates me. how can use observation labels rownames(tmp) in silhouette plot opposed numeric indices (1 12) - make no sense whatsoever me.

enter image description here

i'm not sure why silhouette call seems drop row names. can add them 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)

enter image description here


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