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
|
# library(dendextend)
# library(testthat)
context("Trimming a tree")
test_that("Trimming removes leaves and updates the object", {
assign_dendextend_options()
hc <- hclust(dist(USArrests[1:5, ]), "ave")
dend <- as.dendrogram(hc)
pruned_dend <- prune(dend, c("Alaska", "California"))
expect_equal(nleaves(dend), 5L)
expect_equal(nleaves(pruned_dend), 3L) # we pruned two leaves
expect_equal(attr(pruned_dend, "members"), 3L) # checking the attributes are correct.
expect_equal(attr(dend, "height"), attr(pruned_dend, "height")) # root height should not change due to this specific pruning
expect_true(all(labels(pruned_dend) %in% labels(dend)))
expect_warning(prune(dend, c("non-existing leaf")))
})
test_that("Trimming works for unbranched trees", {
assign_dendextend_options()
hc <- hclust(dist(USArrests[1:5, ]), "ave")
dend <- as.dendrogram(hc)
unbranched_dend <- unbranch(dend, 2)
pruned_unbranched_dend <- prune(unbranched_dend, c("Alaska", "California"))
expect_equal(nleaves(pruned_unbranched_dend), 3L)
expect_equal(attr(pruned_unbranched_dend, "members"), 3L) # checking the attributes are correct.
expect_true(all(labels(pruned_unbranched_dend) %in% labels(dend)))
expect_warning(prune(unbranched_dend, c("non-existing leaf")))
})
test_that("Intersecting-trees works", {
assign_dendextend_options()
hc_1 <- hclust(dist(USArrests[1:5, ]), "single")
hc_2 <- hclust(dist(USArrests[1:5, ]), "complete")
dend_1 <- as.dendrogram(hc_1)
dend_2 <- as.dendrogram(hc_2)
pruned_dend_1 <- prune(dend_1, c("Alaska"))
pruned_dend_2 <- prune(dend_2, c("California"))
dends_12 <- intersect_trees(pruned_dend_1, pruned_dend_2)
expect_equal(length(dends_12), 2L)
expect_equal(nleaves(dends_12[[1]]), 3L) # 3 leaves - tree 1
expect_equal(nleaves(dends_12[[2]]), 3L) # 3 leaves - tree 2
expect_equal(
length(
intersect(labels(dends_12[[1]]), labels(dends_12[[2]]))
),
3L
) # 3 labels are the same for both trees.
# that it returns the same object
dends_11 <- intersect_trees(dend_1, dend_1)
expect_identical(dends_11[[1]], dend_1)
})
test_that("Trimming works for non-binary trees", {
assign_dendextend_options()
## Simplest case: A flat, non-binary dendrogram
hc <- hclust(dist(iris[1:5, -5]))
dend_a <- as.dendrogram(hc)
dend_a <- collapse_branch(dend_a, tol = 0.5)
# Remove 1 non-binary leaf
targets_1 <- c("2")
pruned_dend_1 <- prune(dend_a, targets_1)
# Since this is flat, expect a length of 5 - 1 = 4
expect_equal(length(pruned_dend_1), 4L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_1), setdiff(labels(dend_a), targets_1))
# Remove multiple non-binary leaves
targets_2 <- c("2", "5")
pruned_dend_2 <- prune(dend_a, targets_2)
# Since this is flat, expect a length of 5 - 2 = 3
expect_equal(length(pruned_dend_2), 3L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_2), setdiff(labels(dend_a), targets_2))
## A more complex example
hc <- hclust(dist(iris[1:15, -5]))
dend_b <- as.dendrogram(hc)
dend_b <- collapse_branch(dend_b, tol = 0.3)
# Remove 1 non-binary leaf in a terminal node
targets_3 <- c("2")
pruned_dend_3 <- prune(dend_b, targets_3)
# The top of the dend shouldn't change, so length is 2
expect_equal(length(pruned_dend_3), 2L)
# N Leaves should now be reduced. 15 - 1 = 14
expect_equal(nleaves(pruned_dend_3), 14L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_3), setdiff(labels(dend_b), targets_3))
# Remove multiple non-binary leaves in a terminal node
targets_4 <- c("2", "10", "13")
pruned_dend_4 <- prune(dend_b, targets_4)
# The top of the dend shouldn't change, so length is 2
expect_equal(length(pruned_dend_4), 2L)
# N Leaves should now be reduced. 15 - 3 = 12
expect_equal(nleaves(pruned_dend_4), 12L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_4), setdiff(labels(dend_b), targets_4))
# Remove all but one leaf from a non-binary node
# Should merge up to the next level.
targets_5 <- c("2", "3", "4", "10")
pruned_dend_5 <- prune(dend_b, targets_5)
# The top of the dend shouldn't change, so length is 2
expect_equal(length(pruned_dend_5), 2L)
# N Leaves should now be reduced. 15 - 4 = 11
expect_equal(nleaves(pruned_dend_5), 11L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_5), setdiff(labels(dend_b), targets_5))
# The remaining leaf, 13, was originally at:
# dend[[2]][[2]][[1]][[2]][[3]]
expect_true("13" == labels(dend_b[[2]][[2]][[1]][[2]][[3]]))
expect_false(is.leaf(dend_b[[2]][[2]][[1]][[2]])) # This is the node with the non-binary split
# The remaining leaf, 13, should now move up to:
# dend[[2]][[2]][[1]][[2]]
expect_true("13" == labels(pruned_dend_5[[2]][[2]][[1]][[2]]))
expect_true(is.leaf(pruned_dend_5[[2]][[2]][[1]][[2]])) # This should now be true.
# Remove a non-binary leaf from an upper branch
targets_6 <- "1"
pruned_dend_6 <- prune(dend_b, targets_6)
# The top of the dend shouldn't change, so length is 2
expect_equal(length(pruned_dend_6), 2L)
# N Leaves should now be reduced. 15 - 1 = 14
expect_equal(nleaves(pruned_dend_6), 14L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_6), setdiff(labels(dend_b), targets_6))
# Remove multiple non-binary leaves from an upper branch
targets_7 <- c("1", "5")
pruned_dend_7 <- prune(dend_b, targets_7)
# The top of the dend shouldn't change, so length is 2
expect_equal(length(pruned_dend_7), 2L)
# N Leaves should now be reduced. 15 - 2 = 13
expect_equal(nleaves(pruned_dend_7), 13L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_7), setdiff(labels(dend_b), targets_7))
# dend_b[[2]][[2]] should now be binary
expect_equal(length(dend_b[[2]][[2]]), 4L)
expect_equal(length(pruned_dend_7[[2]][[2]]), 2L)
# Remove all non-binary leaves from an upper branch
targets_8 <- c("1", "5", "8")
pruned_dend_8 <- prune(dend_b, targets_8)
# The top of the dend shouldn't change, so length is 2
expect_equal(length(pruned_dend_8), 2L)
# N Leaves should now be reduced. 15 - 3 = 12
expect_equal(nleaves(pruned_dend_8), 12L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_8), setdiff(labels(dend_b), targets_8))
# The branch at dend_b[[2]][[2]] should merge up and should have length 2, with 7 leaves
expect_equal(length(pruned_dend_8[[2]][[2]]), 2L)
expect_equal(nleaves(pruned_dend_8[[2]][[2]]), 7L)
# Max depth for this branching should be reduced by 1
expect_true(is.leaf(dend_b[[2]][[2]][[1]][[1]][[1]]))
expect_true(is.leaf(pruned_dend_8[[2]][[2]][[1]][[1]]))
# Remove non-binary and binary branches from multiple levels in one go
targets_9 <- c("6", "14", "13", "8")
pruned_dend_9 <- prune(dend_b, targets_9)
# The top of the dend shouldn't change, so length is 2
expect_equal(length(pruned_dend_9), 2L)
# N Leaves should now be reduced. 15 - 4 = 11
expect_equal(nleaves(pruned_dend_9), 11L)
# Labels should transfer as expected
expect_equal(labels(pruned_dend_9), setdiff(labels(dend_b), targets_9))
})
# unbranched_dend <- unbranch(dend,2)
# pruned_dend <- prune(unbranched_dend , c("Alaska", "California"))
# str(unclass(pruned_dend))
# str(unclass(unbranched_dend))
# plot(unbranched_dend)
# plot(pruned_dend)
#
#
|
