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# library(testthat)
context("Untangle two dendrograms for plotting a tanglegram")
test_that("shuffle works", {
suppressWarnings(RNGversion("3.5.0"))
# library(magrittr)
dend <- USArrests %>%
dist() %>%
hclust() %>%
as.dendrogram()
set.seed(234238)
dend2 <- dend %>% shuffle()
# different tree layouts:
# tanglegram(dend, dend2, margin_inner=7)
expect_identical(round(entanglement(dend, dend2), 3), 0.398)
expect_false(identical(dend, dend2))
# same topology
expect_true(identical(sort(dend), sort(dend2)))
dend12 <- dendlist(dend, dend2)
expect_false(identical(dend12, shuffle(dend12)))
expect_equal(length(shuffle(dend12)), 2)
})
test_that("Flip leaves work", {
dend1 <- USArrests[1:5, ] %>%
dist() %>%
hclust() %>%
as.dendrogram()
dend2 <- flip_leaves(dend1, c(3, 5), c(1, 2))
# tanglegram(dend1,dend2)
# tanglegram(dend1,flip_leaves(dend1, c(3,5, 1,2), c(4)))
expect_identical(entanglement(dend1, dend2, L = 2), 0.4)
})
test_that("all_couple_rotations_at_k work", {
dend1 <- USArrests[1:5, ] %>%
dist() %>%
hclust() %>%
as.dendrogram()
dend2 <- all_couple_rotations_at_k(dend1, k = 2)[[2]]
# tanglegram(dend1,dend2)
expect_identical(entanglement(dend1, dend2, L = 2), 0.5)
})
test_that("untangle_step_rotate_1side work", {
suppressWarnings(RNGversion("3.5.0"))
dend1 <- USArrests[1:10, ] %>%
dist() %>%
hclust() %>%
as.dendrogram()
set.seed(3525)
dend2 <- shuffle(dend1)
# tanglegram(dend1,dend2)
expect_identical(round(entanglement(dend1, dend2, L = 2), 2), 0.47)
# Fixing the problem :)
dend2_corrected <- untangle_step_rotate_1side(dend2, dend1)[[1]]
# tanglegram(dend1,dend2_corrected) # FIXED.
expect_identical(round(entanglement(dend1, dend2_corrected, L = 2), 2), 0)
# the other direction may also work:
dend2_corrected <- untangle_step_rotate_1side(dend2, dend1, direction = "backward")[[1]]
# tanglegram(dend1,dend2_corrected) # FIXED.
expect_identical(round(entanglement(dend1, dend2_corrected, L = 2), 2), 0)
})
test_that("untangle_step_rotate_2side work", {
suppressWarnings(RNGversion("3.5.0"))
dend1 <- USArrests[1:10, ] %>%
dist() %>%
hclust() %>%
as.dendrogram()
set.seed(3525645)
dend2 <- USArrests[1:10, ] %>%
dist() %>%
hclust(method = "med") %>%
as.dendrogram() %>%
shuffle()
# tanglegram(dend1,dend2)
dend1 <- sort(dend1)
dend2 <- sort(dend2)
expect_identical(round(entanglement(dend1, dend2, L = 2), 2), 0.21)
# this is behaving different for R 3.3.3 and 3.4 - I'm not sure why...
#
# # Fixing the problem :)
# dend12_corrected <- suppressWarnings(
# untangle_step_rotate_2side(dend1, dend2, L = 2, print_times=FALSE, max_n_iterations = 20)
# )
#
# # tanglegram(dend12_corrected[[1]],dend12_corrected[[2]]) # FIXED.
# expect_identical(round(entanglement(dend12_corrected[[1]],dend12_corrected[[2]], L = 2),3) , 0.036)
#
#
})
#
# # This one is an example of how 2side rotation is better. But it takes longer
# # So I don't run it:
#
# test_that("untangle_step_rotate_2side works better than 1side",{
#
#
# dend1 <- as.dendrogram(hclust(dist(USArrests[1:20,])))
# dend2 <- as.dendrogram(hclust(dist(USArrests[1:20,]), method = "single"))
# set.seed(3525)
# dend2 <- shuffle(dend2)
# # tanglegram(dend1,dend2, margin_inner=6.5)
# expect_identical(round(entanglement(dend1,dend2, L = 2),2) , 0.79)
#
# dend2_corrected <- untangle_step_rotate_1side(dend2, dend1)
# # tanglegram(dend1,dend2_corrected, margin_inner=6.5) # Good.
# expect_identical(round(entanglement(dend1,dend2_corrected, L = 2),3) , 0.007)
# # it is better, but not perfect. Can we improve it?
#
# dend12_corrected <- untangle_step_rotate_2side(dend1, dend2,print_times=FALSE)
# # tanglegram(dend12_corrected[[1]],dend12_corrected[[2]], margin_inner=6.5) # Better...
# expect_identical(round(entanglement(dend12_corrected[[1]],dend12_corrected[[2]], L=2),3) , 0.005)
#
# # best combination:
# dend12_corrected_1 <- untangle_random_search(dend1, dend2)
# dend12_corrected_2 <- untangle_step_rotate_2side(dend12_corrected_1[[1]],dend12_corrected_1[[2]],print_times=FALSE)
# # tanglegram(dend12_corrected_2[[1]],dend12_corrected_2[[2]], margin_inner=6.5) # Better...
# expect_identical(round(entanglement(dend12_corrected_2[[1]],dend12_corrected_2[[2]], L=2),3) , 0)
# # 0 - PERFECT.
#
# })
#
test_that("untangle (main function) works for random search", {
suppressWarnings(RNGversion("3.5.0"))
dend1 <- USArrests[1:5, ] %>%
dist() %>%
hclust() %>%
as.dendrogram()
dend2 <- flip_leaves(dend1, c(3, 5), c(1, 2))
# tanglegram(dend1,dend2)
# tanglegram(dend1,flip_leaves(dend1, c(3,5, 1,2), c(4)))
dend12 <- dendlist(dend1, dend2)
set.seed(123123)
out1 <- untangle(dend12, method = "ran", R = 10)
set.seed(123123)
out2 <- untangle_random_search(dend1, dend2, R = 10)
expect_identical(out1, out2)
})
test_that("untangle (main function) works for 2 step", {
suppressWarnings(RNGversion("3.5.0"))
dend1 <- USArrests[1:5, ] %>%
dist() %>%
hclust() %>%
as.dendrogram()
dend2 <- flip_leaves(dend1, c(3, 5), c(1, 2))
# tanglegram(dend1,dend2)
# tanglegram(dend1,flip_leaves(dend1, c(3,5, 1,2), c(4)))
dend12 <- dendlist(dend1, dend2)
out1 <- untangle(dend12, method = "step2")
set.seed(123123)
out2 <- untangle_step_rotate_2side(dend1, dend2)
expect_identical(out1, out2)
})
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