cutree for dendrogram (by 1 k value only!)

Cuts a dendrogram tree into several groups by specifying the desired number of clusters k (only a single k value!).

In case there exists no such k for which exists a relevant split of the dendrogram, a warning is issued to the user, and NA is returned.

cutree_1k.dendrogram(
  dend,
  k,
  dend_heights_per_k = NULL,
  use_labels_not_values = TRUE,
  order_clusters_as_data = TRUE,
  warn = dendextend_options("warn"),
  ...
)

Arguments

dend

a dendrogram object

k

numeric scalar (not a vector!) with the number of clusters the tree should be cut into.

dend_heights_per_k

a named vector that resulted from running. heights_per_k.dendrogram. When running the function many times, supplying this object will help improve the running time.

use_labels_not_values

logical, defaults to TRUE. If the actual labels of the clusters do not matter - and we want to gain speed (say, 10 times faster) - then use FALSE (gives the "leaves order" instead of their labels.). This is passed to cutree_1h.dendrogram.

order_clusters_as_data

logical, defaults to TRUE. There are two ways by which to order the clusters: 1) By the order of the original data. 2) by the order of the labels in the dendrogram. In order to be consistent with cutree, this is set to TRUE. This is passed to cutree_1h.dendrogram.

warn

logical (default from dendextend_options("warn") is FALSE). Set if warning are to be issued, it is safer to keep this at TRUE, but for keeping the noise down, the default is FALSE. Should the function send a warning in case the desried k is not available?

...

(not currently in use)

Value

cutree_1k.dendrogram returns an integer vector with group memberships.

In case there exists no such k for which exists a relevant split of the dendrogram, a warning is issued to the user, and NA is returned.

See also

hclust, cutree, cutree_1h.dendrogram

Author

Tal Galili

Examples

hc <- hclust(dist(USArrests[c(1, 6, 13, 20, 23), ]), "ave")
dend <- as.dendrogram(hc)
cutree(hc, k = 3) # on hclust
#>   Alabama  Colorado  Illinois  Maryland Minnesota 
#>         1         1         1         2         3 
cutree_1k.dendrogram(dend, k = 3) # on a dendrogram
#>   Alabama  Colorado  Illinois  Maryland Minnesota 
#>         1         1         1         2         3 

labels(dend)
#> [1] "Minnesota" "Maryland"  "Colorado"  "Alabama"   "Illinois" 

# the default (ordered by original data's order)
cutree_1k.dendrogram(dend, k = 3, order_clusters_as_data = TRUE)
#>   Alabama  Colorado  Illinois  Maryland Minnesota 
#>         1         1         1         2         3 

# A different order of labels - order by their order in the tree
cutree_1k.dendrogram(dend, k = 3, order_clusters_as_data = FALSE)
#> Minnesota  Maryland  Colorado   Alabama  Illinois 
#>         3         2         1         1         1 


# make it faster
if (FALSE) { # \dontrun{
library(microbenchmark)
dend_ks <- heights_per_k.dendrogram
microbenchmark(
  cutree_1k.dendrogram = cutree_1k.dendrogram(dend, k = 4),
  cutree_1k.dendrogram_no_labels = cutree_1k.dendrogram(dend,
    k = 4, use_labels_not_values = FALSE
  ),
  cutree_1k.dendrogram_no_labels_per_k = cutree_1k.dendrogram(dend,
    k = 4, use_labels_not_values = FALSE,
    dend_heights_per_k = dend_ks
  )
)
# the last one is the fastest...
} # }