1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340
|
# Copyright (C) Tal Galili
#
# This file is part of dendextend.
#
# dendextend is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# dendextend is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
#' @title get attributes from the dendrogram's root(!) branches
#' @description get attributes from the dendrogram's root(!) branches
#' @export
#' @param dend dendrogram object
#' @param the_attr the attribute to get from the branches (for example "height")
#' @param 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 a warning be printed when
#' the function is used on an object which is NOT a dendrogram.
#' @param ... passed on to attr
#' @return The attributes of the branches (often two) of the dendrogram's root
#' @seealso \link{attr}
#' @examples
#' hc <- hclust(dist(USArrests[2:9,]), "com")
#' dend <- as.dendrogram(hc)
#'
#' get_root_branches_attr(dend, "height") # 0.00000 71.96247
#' # plot(dend)
#' str(dend, 2)
get_root_branches_attr <- function(dend, the_attr, warn = dendextend_options("warn"),...) {
if(!is.dendrogram(dend))
{
if(warn) warning("dend wasn't of class dendrogram - be sure it makes sense...")
# I might make this S3 at some point, but I don't see a need for it...
# class(dend) <- "dendrogram"
# dend <- as.dendrogram(dend)
}
sapply(dend, function(x) {attr(x, the_attr,...)})
}
#' @title Raise the height of a dendrogram tree
#' @description Raise the height of nodes in a dendrogram tree.
#' @export
#' @param dend dendrogram object
#' @param heiget_to_add how much height to add to all the branches (not leaves) in the dendrogram
#' @param ... passed on (not used)
#' @return A raised dendrogram
#' @examples
#' hc <- hclust(dist(USArrests[2:9,]), "com")
#' dend <- as.dendrogram(hc)
#'
#' par(mfrow = c(1,2))
#' plot(dend, main = "original tree")
#' plot(raise.dendrogram(dend , 100), main = "Raised tree")
raise.dendrogram <- function(dend, heiget_to_add,...)
{
# Only if you are not a leaf - then do things
if(!is.leaf(dend))
{
# first - move through all the branches and implement this function on them (they will return higher...
num_of_branches <- length(dend)
for(i in seq_len(num_of_branches))
{
dend[[i]] <- raise.dendrogram(dend[[i]], heiget_to_add) # go into the tree with recursion...
}
# change the height of our current branch
attr(dend, "height") <- attr(dend, "height") + heiget_to_add
}
return(dend)
}
#' @title unbranch trees
#' @description unbranch trees and merges the subtree to the parent node.
#' @export
#' @rdname unbranch
#'
#' @param dend a dendrogram (or hclust) object
#' @param branch_becoming_root a numeric choosing the branch of the root which will become the new root (from left to right)
#' @param new_root_height the new height of the branch which will become the new root.
#' If the parameter is not given - the height of the original root is used.
#' @param ... passed on
#' @return An unbranched dendrogram
#' @seealso \link[ape]{unroot} {ape}
#' @examples
#' hc <- hclust(dist(USArrests[2:9,]), "com")
#' dend <- as.dendrogram(hc)
#'
#' par(mfrow = c(1,3))
#' plot(dend, main = "original tree")
#' plot(unbranch(dend , 1), main = "unbranched tree (left branch)")
#' plot(unbranch(dend , 2), main = "tree without (right branch)")
unbranch <- function(dend, ...) {
UseMethod("unbranch")
}
#' @export
#' @rdname unbranch
unbranch.default <- function(dend,...) stop("object dend must be a dendrogram/hclust/phylo object")
#' @export
#' @rdname unbranch
unbranch.dendrogram <- function(dend, branch_becoming_root = 1, new_root_height,...)
{
# dend <- x # (since this function is based on dendrograms)
if(is.leaf(dend[[branch_becoming_root]])) {
warning("unbranch.dendrogram can't have the new root being a leaf.
The original dendrogram is returned.
Please choose another branch to be the root.")
return(dend)
}
new_dend <- list()
i_new_dend_branch <- 1
# add branches from the new root branch to the new tree
number_of_branches_in_root <- length(dend[[branch_becoming_root]])
for(i in seq_len(number_of_branches_in_root))
{
new_dend[[i_new_dend_branch]] <- dend[[branch_becoming_root]][[i]] # add the branches of the branc_becoming_root to the new tree
i_new_dend_branch <- i_new_dend_branch + 1
}
# add all other branches of the old tree to the root of the new tree
number_of_branches_in_dend <- length(dend)
number_of_branches_in_dend_minus_root <- number_of_branches_in_dend- 1
branches_to_add_to_root <- seq_len(number_of_branches_in_dend)[-branch_becoming_root]
# id of branches to add to the root of the new tree
for(i in seq_len(number_of_branches_in_dend_minus_root))
{
new_dend[[i_new_dend_branch]] <- dend[[branches_to_add_to_root[i] ]] # add the branches of the branc_becoming_root to the new tree
i_new_dend_branch <- i_new_dend_branch + 1
}
# set the proper attributes of the root of the new tree
if(!missing(new_root_height)){
attr(new_dend, "height") <- new_root_height
} else {
attr(new_dend, "height") <- attr(dend, "height") # + attr(dend[[branch_becoming_root]], "height")
}
class(new_dend) <- 'dendrogram'
attr(new_dend, "members") <- sum(get_root_branches_attr(new_dend, "members")) # the new members of the root is the sum of the members in all of his branches
attr(new_dend, "midpoint") <-
suppressWarnings(mean(get_root_branches_attr(new_dend, "midpoint"), na.rm = TRUE) )
# the new midpoint of the root is the mean of the midpoint in all of his branches
# if some are NA, they are ignored
# Bad idea: we only use labels for the leafs...
# attr(new_dend, "label") <- "merged root" # might cause problems in the future?
new_dend <- suppressWarnings(stats_midcache.dendrogram(new_dend)) # might through warnings if we have 3 branches (but it will keep the "midpoints" in check
return(new_dend)
}
#' @export
#' @rdname unbranch
unbranch.hclust <- function(dend, branch_becoming_root = 1, new_root_height, ...) {
x_dend <- as.dendrogram(dend)
x_dend_unbranch <- unbranch(x_dend, branch_becoming_root , new_root_height, ...)
x_unbranch <- as_hclust_fixed(x_dend_unbranch, dend)
return(x_unbranch)
}
#' @export
#' @rdname unbranch
unbranch.phylo <- function(dend, ...) {
# ape::unbranch(phy = x)
# library(ape)
x_dend <- as.dendrogram(dend)
x_dend_unbranch <- unbranch(x_dend, ...) # branch_becoming_root , new_root_height,
x_unbranch <- ape::as.phylo(x_dend_unbranch)
return(x_unbranch)
}
#' @title Flatten the branches of a dendrogram's root
#' @description
#' The function makes sure the two branches of the root of a dendrogram will have the same height.
#' The user can choose how to decide which height to use.
#' @export
#' @param dend dendrogram object
#' @param FUN how to choose the new height of both branches (defaults to taking the max between the two)
#' @param new_height overrides FUN, and sets the new height of the two branches manually
#' @param ... passed on (not used)
#' @return A dendrogram with both of the root's branches of the same height
#' @examples
#' hc <- hclust(dist(USArrests[2:9,]), "com")
#' dend <- as.dendrogram(hc)
#' attr(dend[[1]], "height") <- 150 # make the height un-equal
#'
#' par(mfrow = c(1,2))
#' plot(dend, main = "original tree")
#' plot(flatten.dendrogram(dend), main = "Raised tree")
flatten.dendrogram <- function(dend, FUN = max, new_height,...)
{
if(missing(new_height)) {
dend_branches_height <- get_root_branches_attr(dend, "height")
new_height <- FUN(dend_branches_height)
}
for(i in seq_len(length(dend))) attr(dend[[i]], "height") <- new_height
return(dend)
}
# get_all_leaves(dend)
get_all_leaves <- function(dend, ...) {
leaves <- as.list(rep(NA, nleaves(dend)))
# this function is used to modify object_attr. What it returns is not important.
i_leaf <- 0
get_attr_from_node <- function(dend_node) {
if(is.leaf(dend_node)) {
i_leaf <<- i_leaf + 1
leaves[[i_leaf]] <<- unclass(dend_node)
}
return(invisible())
}
dendrapply(dend, get_attr_from_node)
leaves
}
#' @title Collapse branches under a tolerance level
#' @description
#' Collapse branches under a tolerance level
#' @export
#' @param dend dendrogram object
#' @param tol a numeric value giving the tolerance to consider a branch length significantly greater than zero
#' @param lower logical (TRUE). collapse branches which are lower than tol?
#' @param ... passed on (not used)
#' @return A dendrogram with both of the root's branches of the same height
#' @seealso \link[ape]{multi2di}
#' @examples
#'
#' # # ladderize is like sort(..., type = "node")
#' dend <- iris[1:5,-5] %>% dist %>% hclust %>% as.dendrogram
#' par(mfrow = c(1,3))
#' dend %>% ladderize %>% plot(horiz = TRUE); abline(v = .2, col = 2, lty = 2)
#' dend %>% collapse_branch(tol = 0.2) %>% ladderize %>% plot(horiz = TRUE)
#' dend %>% collapse_branch(tol = 0.2) %>% ladderize %>%
#' hang.dendrogram(hang = 0) %>% plot(horiz = TRUE)
#'
#' par(mfrow = c(1,2))
#' dend %>% collapse_branch(tol = 0.2, lower = FALSE) %>% plot(horiz = TRUE, main = "dendrogram")
#' library(ape)
#' dend %>% as.phylo %>% di2multi(tol = 0.2) %>% plot(main = "phylo")
collapse_branch <- function(dend, tol = 1e-08, lower = TRUE, ...)
{
if(!is.dendrogram(dend)) stop("'dend' should be a dendrogram.")
if(nleaves(dend) == 1) {
warning("nleaves(dend) == 1 - returning dend")
if(attr(dend, "height") < tol) warning("dend height < tol")
return(dend)
}
fix_height_attr_per_node <- function(dend_node)
{
if(is.leaf(dend_node)) return(unclass(dend_node))
the_leaves <- list()
nodes_to_rm <- NULL
for(i_nodes in seq_len(length(dend_node))) {
a_leaf <- is.leaf(dend_node[[i_nodes]])
short <- attr(dend_node[[i_nodes]], "height") < tol
if(!lower) short <- !short
if(!a_leaf & short) {
the_leaves <- c(the_leaves, get_all_leaves(dend_node[[i_nodes]]))
nodes_to_rm <- c(nodes_to_rm, i_nodes)
} else {
dend_node[[i_nodes]] <- fix_height_attr_per_node(dend_node[[i_nodes]])
}
}
if(!is.null(nodes_to_rm)) {
tmp_attr <- attributes(dend_node)
dend_node <- c(dend_node, the_leaves)
dend_node <- dend_node[-nodes_to_rm]
attributes(dend_node) <- tmp_attr
}
return(unclass(dend_node))
}
dend <- fix_height_attr_per_node(dend)
class(dend) <- "dendrogram"
dend <- suppressWarnings(stats_midcache.dendrogram(dend)) # might through warnings if we have 3 branches (but it will keep the "midpoints" in check
return(dend)
}
#TODO: add tests
|