Nothing
library("TreeTools")
test_that("VisualizeMatching() works", {
tree1 <- PectinateTree(1:11)
tree2 <- tree1
tree2$tip.label[c(11, 1)] <- tree1$tip.label[c(1, 11)]
tree2r <- CollapseNode(tree2, 20:21)
Minus <- function(...) {
x <- MutualClusteringInfo(...)
attr(x, "pairScores") <- -attr(x, "pairScores")
x
}
expect_error(VisualizeMatching(Minus, PectinateTree(8), BalancedTree(8),
setPar = FALSE))
skip_if_not_installed("vdiffr")
skip_if(packageVersion("graphics") < "4.3")
skip_if(packageVersion("vdiffr") < "1.0")
TestVM <- function() {
VisualizeMatching(MutualClusteringInfo, tree1, tree2,
setPar = TRUE, precision = 3, matchZeros = FALSE,
Plot = plot.phylo)
}
vdiffr::expect_doppelganger("Test VM", TestVM)
TestVMr <- function() {
VisualizeMatching(MutualClusteringInfo, tree1, tree2r,
setPar = TRUE, precision = 3, matchZeros = TRUE,
Plot = plot.phylo, cex = 1.5)
}
vdiffr::expect_doppelganger("Test VMr", TestVMr)
vdiffr::expect_doppelganger("Visualize MCI matching", function() {
par(mfrow = c(2, 2), mar = rep(0.1, 4), cex = 1.5)
tree1 <- ape::read.tree(text="((1, 2), ((3, (4, 5)), (6, (7, (8, 9)))));")
tree2 <- ape::read.tree(text="((1, 2), ((3, 4, (5, 9)), (6, (7, 8))));")
VisualizeMatching(MutualClusteringInfo, tree1, tree2,
setPar = FALSE, precision = 3L,
Plot = TreeDistPlot,
matchZeros = FALSE,
leaveRoom = FALSE)
VisualizeMatching(MutualClusteringInfo, tree2, tree1,
setPar = FALSE, precision = 3,
Plot = TreeDistPlot,
matchZeros = FALSE,
leaveRoom = FALSE)
})
vdiffr::expect_doppelganger("RF: Collapse a node", function() {
par(mfrow = c(2, 2), mar = rep(0.1, 4), cex = 1.5)
tree1 <- ape::read.tree(text="((1, 2), ((6, (7, 8)), (3, 4, (5, 9))));")
tree2 <- ape::read.tree(text="((1, 2), ((3, (4, (5, 9))), (6, (7, 8))));")
VisualizeMatching(RobinsonFouldsMatching, tree1, tree2,
setPar = FALSE, precision = 3,
Plot = TreeDistPlot,
matchZeros = TRUE,
leaveRoom = FALSE)
VisualizeMatching(RobinsonFouldsMatching, tree2, tree1,
setPar = FALSE, precision = 3,
Plot = TreeDistPlot,
matchZeros = FALSE,
leaveRoom = FALSE)
})
vdiffr::expect_doppelganger("RF: Collapse and change", function() {
par(mfrow = c(2, 2), mar = rep(0.1, 4), cex = 1.5)
tree1 <- ape::read.tree(text="((1, 2), ((6, (7, 8)), (3, 4, (5, 9))));")
tree2 <- ape::read.tree(text="((1, 2), ((3, (4, (5, 9))), ((6, 7), 8)));")
VisualizeMatching(RobinsonFouldsMatching, tree1, tree2,
setPar = FALSE, precision = 3L,
Plot = TreeDistPlot,
matchZeros = TRUE,
leaveRoom = FALSE)
VisualizeMatching(RobinsonFouldsMatching, tree2, tree1,
setPar = FALSE, precision = 3L,
Plot = TreeDistPlot,
matchZeros = FALSE,
leaveRoom = FALSE)
})
vdiffr::expect_doppelganger("RF VM Single splits; plainEdges", function() {
par(mfrow = c(2, 2), mar = rep(0.1, 4), cex = 1.5)
tree1 <- ape::read.tree(text = "((1, 2), (3, 4, 5, 6, 7, 8));")
tree2 <- ape::read.tree(text = "((1, 2, 3), (4, 5, 6, 7, 8));")
VisualizeMatching(RobinsonFouldsMatching, tree1, tree2,
setPar = FALSE,
Plot = TreeDistPlot,
matchZeros = TRUE,
plainEdges = TRUE,
edge.width = NULL,
leaveRoom = FALSE)
VisualizeMatching(RobinsonFouldsMatching, tree2, tree1,
setPar = FALSE,
Plot = TreeDistPlot,
matchZeros = FALSE,
plainEdges = FALSE,
leaveRoom = FALSE)
})
vdiffr::expect_doppelganger("JRF VM matchZeros FALSE", function() {
JRF2 <- function(tree1, tree2, ...)
JaccardRobinsonFoulds(tree1, tree2, k = 2, allowConflict = FALSE, ...)
tree1 <- RootTree(as.phylo(704564, 10), paste0("t", c(1, 4, 5, 8, 9)))
tree2 <- RootTree(as.phylo(20165 , 10), paste0("t", c(1, 4)))
VisualizeMatching(JRF2, tree1, tree2, matchZeros = FALSE)
})
})
test_that("VisualizeMatching() handles unrooted trees", {
skip_if_not_installed("graphics", "4.3")
skip_if_not_installed("vdiffr", "1.0")
vdiffr::expect_doppelganger("VM unrooted", function() {
par(mfrow = c(2, 2), mar = rep(0.1, 4), cex = 1.5)
tree1 <- UnrootTree(BalancedTree(1:5))
tree2 <- UnrootTree(PectinateTree(1:5))
VisualizeMatching(RobinsonFouldsMatching, tree1, tree2,
setPar = FALSE,
Plot = TreeDistPlot)
})
vdiffr::expect_doppelganger("VM one rooted", function() {
par(mfrow = c(2, 2), mar = rep(0.1, 4), cex = 1.5)
tree1 <- UnrootTree(BalancedTree(1:5))
tree2 <- PectinateTree(1:5)
VisualizeMatching(RobinsonFouldsMatching, tree1, tree2,
setPar = FALSE,
Plot = TreeDistPlot)
})
})
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