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
|
# 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 Find which nodes satisfies a condition
#' @export
#' @description
#' Goes through a tree's nodes in order to return a vector
#' with whether (TRUE/FALSE) each node satisies some condition (function)
#'
#' @param dend a dendrogram dend
#' @param condition a function that gets a node and return TRUE or FALSE
#' (based on whether or not that node/tree fulfills the "condition")
#' @param include_leaves logical. Should leaves attributes be included as well?
#' @param include_branches logical. Should non-leaf (branch node)
#' attributes be included as well?
#' @param na.rm logical. Should NA attributes be REMOVED from the resulting vector?
#' @param ... passed to the condition function
#' @return
#' A logical vector with TRUE/FALSE, specifying for each of the dendrogram's nodes if it fulfills the condition or not.
#' @seealso \link{branches_attr_by_labels}, \link{get_leaves_attr}, \link{nnodes}, \link{nleaves}
#' @examples
#' \dontrun{
#'
#' library(dendextend)
#'
#' set.seed(23235)
#' ss <- sample(1:150, 10)
#'
#' # Getting the dend dend
#' dend <- iris[ss, -5] %>%
#' dist() %>%
#' hclust() %>%
#' as.dendrogram()
#' dend %>% plot()
#'
#'
#'
#' # this is the basis for branches_attr_by_labels
#' has_any_labels <- function(sub_dend, the_labels) any(labels(sub_dend) %in% the_labels)
#' cols <- noded_with_condition(dend, has_any_labels,
#' the_labels = c("126", "109", "59")
#' ) %>%
#' ifelse(2, 1)
#' set(dend, "branches_col", cols) %>% plot()
#'
#' # Similar to branches_attr_by_labels - but for heights!
#' high_enough <- function(sub_dend, height) attr(sub_dend, "height") > height
#' cols <- noded_with_condition(dend, high_enough, height = 1) %>% ifelse(2, 1)
#' set(dend, "branches_col", cols) %>% plot()
#' }
#'
noded_with_condition <- function(dend, condition, include_leaves = TRUE,
include_branches = TRUE,
na.rm = FALSE, ...) {
if (!is.dendrogram(dend)) warning("'dend' should be a dendrogram.")
if (missing(condition)) stop("'condition' parameter is missing.")
dend_cond <- rep(NA, nnodes(dend))
# this function is used to modify dend_cond. What it returns is not important.
i_cond <- 0
check_condition_per_node <- function(dend_node) {
i_cond <<- i_cond + 1
# if we should not include_leaves, then we skip when a leaf is encountered.
if (!include_leaves && is.leaf(dend_node)) {
return(NULL)
}
if (!include_branches && !is.leaf(dend_node)) {
return(NULL)
}
dend_cond[i_cond] <<- condition(dend_node, ...)
return(NULL)
}
dendrapply(dend, check_condition_per_node)
# as.vector is to remove all classes of the na.omit
# thank you Prof. Brian Ripley http://tolstoy.newcastle.edu.au/R/e2/devel/07/01/1965.html
if (na.rm) dend_cond <- as.vector(na.omit(dend_cond))
return(dend_cond)
}
#' @title Which node is a leaf?
#' @export
#' @description
#' Gives a vector as the number of nodes (\link{nnodes}),
#' which gives a TRUE when a node is a leaf.
#' @param dend a dendrogram dend
#' @param ... ignored.
#' @return
#' A logical vector with the length of \link{nnodes},
#' which gives a TRUE when a node is a leaf.
#' @seealso \link{noded_with_condition}, \link{is.leaf}, \link{nnodes}
#' @examples
#' \dontrun{
#'
#' library(dendextend)
#'
#' # Getting the dend dend
#' set.seed(23235)
#' ss <- sample(1:150, 10)
#' dend <- iris[ss, -5] %>%
#' dist() %>%
#' hclust() %>%
#' as.dendrogram()
#' dend %>% plot()
#'
#' which_leaf(dend)
#' }
which_leaf <- function(dend, ...) {
if (!is.dendrogram(dend)) stop("'dend' should be a dendrogram.")
noded_with_condition(dend, is.leaf)
}
#' @title Which node id is common to a group of labels
#' @export
#' @description
#' This function identifies which edge(s) in a tree has group of labels ("tips") in common.
#' By default it only returns the edge (node) with the heighest id.
#'
#' @param dend a dendrogram dend
#' @param labels a character vector of labels from the tree
#' @param max_id logical (TRUE) - if to return only the max id
#' @param ... ignored.
#'
#' @return
#' An integer with the id(s) of the nodes which includes all of the labels.
#'
#' @seealso \link{noded_with_condition}, \link{branches_attr_by_clusters},
#' \link{nnodes}, \link{branches_attr_by_labels}, \link{get_nodes_attr}
#' \link[ape]{which.edge}
#' @examples
#'
#' dend <- iris[1:10, -5] %>%
#' dist() %>%
#' hclust() %>%
#' as.dendrogram() %>%
#' set("labels", 1:10)
#' dend %>% plot()
#'
#' which_node(dend, c(1, 2), max_id = FALSE)
#' which_node(dend, c(2, 3), max_id = FALSE)
#' which_node(dend, c(2, 3))
#'
#' dend %>% plot()
#' the_h <- get_nodes_attr(dend, "height", which_node(dend, c(4, 6)))
#' the_h
#' abline(h = the_h, lty = 2, col = 2)
#' get_nodes_attr(dend, "height", which_node(dend, c(4, 6)))
#' get_nodes_attr(dend, "members", which_node(dend, c(4, 6)))
which_node <- function(dend, labels, max_id = TRUE, ...) {
tree_has_all_labels <- function(sub_dend, the_labels) all(the_labels %in% labels(sub_dend))
nodes_id <- which(noded_with_condition(dend, tree_has_all_labels, the_labels = labels))
if (max_id) nodes_id <- max(nodes_id)
nodes_id
}
|
