dendextend (version 1.18.1)

get_nodes_attr: Get attributes of dendrogram's nodes

Description

Allows easy access to attributes of branches and/or leaves, with option of returning a vector with/withough NA's (for marking the missing attr value)

Usage

get_nodes_attr(
  dend,
  attribute,
  id,
  include_leaves = TRUE,
  include_branches = TRUE,
  simplify = TRUE,
  na.rm = FALSE,
  ...
)

Value

A vector with the dendrogram's nodes attribute. If an attribute is missing from some nodes, it will return NA in that vector.

Arguments

dend

a dendrogram object

attribute

character scalar of the attribute (attr) we wish to get from the nodes

id

integer vector. If given - only the attr of these nodes id will be returned (via depth first search)

include_leaves

logical. Should leaves attributes be included as well?

include_branches

logical. Should non-leaf (branch node) attributes be included as well?

simplify

logical (default is TRUE). should the result be simplified to a vector (using simplify2array ) if possible? If it is not possible it will return a matrix. When FALSE, a list is returned.

na.rm

logical. Should NA attributes be REMOVED from the resulting vector?

...

not used

See Also

get_leaves_attr, nnodes, nleaves

Examples

# define dendrogram object to play with:
hc <- hclust(dist(USArrests[1:3, ]), "ave")
dend <- as.dendrogram(hc)

# get_leaves_attr(dend) # error :)
get_leaves_attr(dend, "label")
labels(dend, "label")
get_leaves_attr(dend, "height") # should be 0's
get_nodes_attr(dend, "height")


get_leaves_attr(dend, "leaf") # should be TRUE's
get_nodes_attr(dend, "leaf") # conatins NA's


get_leaves_attr(dend, "members") # should be 1's
get_nodes_attr(dend, "members", include_branches = FALSE, na.rm = TRUE) #
get_nodes_attr(dend, "members") #
get_nodes_attr(dend, "members", simplify = FALSE)
get_nodes_attr(dend, "members", include_leaves = FALSE, na.rm = TRUE) #

get_nodes_attr(dend, "members", id = c(1, 3), simplify = FALSE)
get_nodes_attr(dend, "members", id = c(1, 3)) #


hang_dend <- hang.dendrogram(dend)
get_leaves_attr(hang_dend, "height") # no longer 0!
get_nodes_attr(hang_dend, "height") # does not include any 0s!

# does not include leaves values:
get_nodes_attr(hang_dend, "height", include_leaves = FALSE)
# remove leaves values all together:
get_nodes_attr(hang_dend, "height", include_leaves = FALSE, na.rm = TRUE)
if (FALSE) {
library(microbenchmark)
# get_leaves_attr is twice faster than get_nodes_attr
microbenchmark(
  get_leaves_attr(dend, "members"), # should be 1's
  get_nodes_attr(dend, "members", include_branches = FALSE, na.rm = TRUE)
)
}