untangle: untangle dendrograms

In dendextend: Extending 'dendrogram' Functionality in R

untangle dendrograms

Description

One untangle function to rule them all.

This function untangles dendrogram lists (dendlist), Using various heuristics.

Usage

untangle(dend1, ...)

## Default S3 method:
untangle(dend1, ...)

untangle_labels(dend1, dend2, ...)

## S3 method for class 'dendrogram'
untangle(
  dend1,
  dend2,
  method = c("labels", "ladderize", "random", "step1side", "step2side", "stepBothSides",
    "DendSer"),
  ...
)

## S3 method for class 'dendlist'
untangle(
  dend1,
  method = c("labels", "ladderize", "random", "step1side", "step2side", "DendSer"),
  which = c(1L, 2L),
  ...
)

Arguments

dend1	a dendrogram or a dendlist object
...	passed to the relevant untangle function
dend2	A second dendrogram (to untangle against)
method	a character indicating the type of untangle heuristic to use. The options are: ("labels", "ladderize", "random", "step1side", "step2side", "stepBothSides", "DendSer")
which	an integer vector of length 2, indicating which of the trees in the dendlist object should be plotted

Details

This function wraps all of the untangle functions, in order to make it easier to find our about (and use) them.

Value

A dendlist, with two trees after they have been untangled.

If the dendlist was originally larger than 2, it will return the original dendlist but with the relevant trees properly rotate.

Author(s)

Tal Galili

See Also

tanglegram, untangle_random_search, untangle_step_rotate_1side, untangle_step_rotate_2side, untangle_DendSer, entanglement

Examples

## Not run: 
set.seed(23235)
ss <- sample(1:150, 10)
dend1 <- iris[ss, -5] %>%
  dist() %>%
  hclust("com") %>%
  as.dendrogram()
dend2 <- iris[ss, -5] %>%
  dist() %>%
  hclust("sin") %>%
  as.dendrogram()
dend12 <- dendlist(dend1, dend2)

dend12 %>% tanglegram()

untangle(dend1, dend2, method = "random", R = 5) %>% tanglegram()

# it works, and we get something different:
set.seed(1234)
dend12 %>%
  untangle(method = "random", R = 5) %>%
  tanglegram()

set.seed(1234)
# fixes it completely:
dend12 %>%
  untangle(method = "random", R = 5) %>%
  untangle(method = "step1") %>%
  tanglegram()
# not good enough
dend12 %>%
  untangle(method = "step1") %>%
  tanglegram()
# not good enough
dend12 %>%
  untangle(method = "step2") %>%
  tanglegram()
# How we might wish to use it:
set.seed(12777)
dend12 %>%
  untangle(method = "random", R = 1) %>%
  untangle(method = "step2") %>%
  tanglegram()

## End(Not run)

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