Nothing
test_that("PlotCharacter()", {
Character <- function (str, plot = FALSE, edges = FALSE, ...) {
tree <- ape::read.tree(text =
"((((((a, b), c), d), e), f), (g, (h, (i, (j, (k, l))))));")
if (edges) {
tree$edge.length <- rep(2, 22)
}
dataset <- TreeTools::StringToPhyDat(str, tips = tree)
PlotCharacter(tree, dataset,
edge.width = 3, plot = plot, ...)
}
expect_equal(structure(c(FALSE, FALSE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE,
TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE,
TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE,
FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE,
FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE,
TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
TRUE, FALSE, FALSE, FALSE, TRUE, TRUE), .Dim = c(23L, 5L),
.Dimnames = list(NULL, c("-", "0", "1", "2", "3"))),
Character("23--1??--032", updateTips = TRUE))
skip_if_not_installed("vdiffr")
Test <- if (interactive()) {
function (str, edges = FALSE) invisible(Character(str, plot = TRUE, edges = edges))
} else {
function (str, edges = FALSE) {
vdiffr::expect_doppelganger(
paste0("PlotChar_",
gsub("?", "Q",
gsub("(", "d",
gsub(")", "b",
gsub("-", "I", str,
fixed = TRUE), fixed = TRUE), fixed = TRUE), fixed = TRUE)),
function() Character(str, plot = TRUE, edges = edges))
}
}
Test("23--1??--032", edges = TRUE)
Test("23--1??(-0)-(01)32")
Test("23??1????032")
Test("11--????--11")
Test("000011????00")
Test("????????????")
Test("-------?????")
Test("------------")
Test("1234(45)AACGTTT")
# From TGuillerme testing suite:
Test("11-------100")
Test("1100----1100")
Test("000011110000")
Test("1---1111---1")
Test("----1111---1")
Test("01----010101")
Test("01---1010101")
Test("1??--??--100")
Test("21--3??--032")
Test("11--1??--111")
Test("11--1000001-")
Test("01------0101")
Test("110--?---100")
Test("210--100--21")
Test("????----1???")
Test("23--1----032")
Test("1----1----1-")
Test("-1-1-1--1-1-")
Test("--------0101")
Test("10101-----01")
Test("011--?--0011")
Test("110--??--100")
Test("21--1----012")
Test("11----111111")
Test("210210------")
Test("----1111----")
Test("230--??1--32")
Test("023--??1--32")
Test("023-???1--32")
Test("23--1?1--023")
Test("----1010----")
Test("------11---1")
Test("10----11---1")
Test("320--??3--21")
})
test_that("Edge cases work", {
tree <- ape::read.tree(text = "(a, (b, ((c, d), (e, f))));")
dataset <- TreeTools::StringToPhyDat("-01100", tips = tree)
if (interactive()) {
PlotCharacter(tree, dataset)
} else {
expect_equal(c("-" = FALSE, "0" = TRUE, "1" = FALSE),
PlotCharacter(tree, dataset, plot = FALSE)[9, ])
}
tree <- ape::read.tree(text = "(a, (b, (c, (d, (e, f)))));")
dataset <- TreeTools::StringToPhyDat("--0101", tips = tree)
if (interactive()) {
PlotCharacter(tree, dataset)
} else {
expect_equal(cbind("-" = c(1, 1, 0, 0, 0),
"0" = c(0, 0, 1, 1, 1),
"1" = c(0, 0, 1, 1, 1)),
1 * PlotCharacter(tree, dataset, plot = FALSE)[7:11, ])
}
})
test_that("Out-of-sequence works", {
skip_if_not_installed("vdiffr")
vdiffr::expect_doppelganger("PlotChar_out-of-sequence", function () {
PlotCharacter(ape::read.tree(text = "(a, (b, (c, d)));"),
TreeTools::StringToPhyDat("1342",
tips = c("a", "c", "d", "b"))
)}
)
})
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