dendextend: cut_lower_fun – R documentation

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cut_lower_fun

Cut a dendrogram - and run a function on the output

Description

Cuts the dend at height h and returns a list with the FUN function implemented on all the sub trees created by cut at height h. This is used for creating a cutree.dendrogram function, by using the labels function as FUN.

This is the Rcpp version of the function, offering a 10-60 times improvement in speed (depending on the tree size it is used on).

Usage

cut_lower_fun(dend, h, FUN = labels, warn = dendextend_options("warn"), ...)

Arguments

`dend`	a dendrogram object.
`h`	a scalar of height to cut the dend by.
`FUN`	a function to run. (default is "labels")
`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 user be warned if reverting to default?
`...`	passed to FUN.

Value

A list with the output of running FUN on each of the sub dends derived from cutting "dend"

Author(s)

Tal Galili

Examples

dend <- as.dendrogram(hclust(dist(iris[1:4, -5])))
# this is really cool!
cut_lower_fun(dend, .4, labels)
lapply(cut(dend, h = .4)$lower, labels)
cut_lower_fun(dend, .4, order.dendrogram)
## Not run: 
# library(dendextend)
library(dendextendRcpp)
dend_big <- as.dendrogram(hclust(dist(iris[1:150, -5])))
library(microbenchmark)
microbenchmark(old_cut_lower_fun(dend_big, .1),
  dendextendRcpp::dendextendRcpp_cut_lower_fun(dend_big, .1),
  times = 100
)
# about 7-15 times faster. It is faster the larger the tree is, and the lower h is.

## End(Not run)

dendextend

Extending 'dendrogram' Functionality in R

v1.15.1

GPL-2 | GPL-3

Authors

Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Yoav Benjamini [ths], Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Cath [ctb] (https://github.com/CathG), John Ma [ctb] (https://github.com/JohnMCMa), Krzysiek G [ctb] (https://github.com/storaged), Manuela Hummel [ctb] (https://github.com/hummelma), Chase Clark [ctb] (https://github.com/chasemc), Lucas Graybuck [ctb] (https://github.com/hypercompetent), jdetribol [ctb] (https://github.com/jdetribol), Ben Ho [ctb] (https://github.com/SplitInf), Samuel Perreault [ctb] (https://github.com/samperochkin), Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/), David Bradley [ctb] (https://github.com/DBradley27), Houyun Huang [ctb] (https://github.com/houyunhuang)

Initial release

2021-05-08