get_nodes_attr: Get attributes of dendrogram's nodes

In dendextend: Extending 'dendrogram' Functionality in R

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,
  ...
)

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

Value

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

Source

Heavily inspired by the code in the function labels.dendrogram, so credit should go to Martin Maechler.

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)
## Not run: 
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)
)

## End(Not run)

dendextend documentation built on Oct. 13, 2024, 1:06 a.m.