Nothing
context("Testing add_root")
cell_ids <- c("a", "b", "c", "d", "e", "f")
milestone_ids <- c("W", "X", "Y", "Z", "A")
milestone_network <- tribble(
~from, ~to, ~length, ~directed,
"W", "X", 2, TRUE,
"X", "Z", 4, TRUE,
"X", "Y", 3, TRUE,
"Z", "A", 5, TRUE
)
divergence_regions <- tribble(
~divergence_id, ~milestone_id, ~is_start,
"XYZ", "X", TRUE,
"XYZ", "Y", FALSE,
"XYZ", "Z", FALSE
)
milestone_percentages <- tribble(
~cell_id, ~milestone_id, ~percentage,
"a", "W", .9,
"a", "X", .1,
"b", "W", .2,
"b", "X", .8,
"c", "X", .8,
"c", "Z", .2,
"d", "X", .2,
"d", "Y", .7,
"d", "Z", .1,
"e", "X", .3,
"e", "Y", .2,
"e", "Z", .5,
"f", "Z", .8,
"f", "A", .2
)
trajectory <- wrap_data(
id = "test",
cell_ids = cell_ids
) %>% add_trajectory(
milestone_ids = milestone_ids,
milestone_network = milestone_network,
milestone_percentages = milestone_percentages,
divergence_regions = divergence_regions
)
# dynplot::plot_graph(trajectory, label_milestones = TRUE)
test_that("Testing add_root on simple linear trajectory", {
rooted <- add_root(trajectory, root_cell_id = "a")
expect_true(rooted$root_milestone_id == "W")
expect_true(rooted$milestone_network$from[[1]] == "W")
expect_true(all(rooted$milestone_network$from == c("W", "X", "Z", "X")))
expect_true(all(rooted$milestone_network$to == c("X", "Z", "A", "Y")))
rooted <- add_root(trajectory)
expect_error(add_root(trajectory, root_cell_id = "trajectories are cool"))
expect_error(add_root(trajectory, root_milestone_id = "trajectories are cool"))
})
test_that("Testing add_root on a more complex linear trajectory", {
trajectory2 <- wrap_data(cell_ids = "a") %>%
add_trajectory(
milestone_network = tibble(from = c("2", "1", "4", "3"), to = c("1", "4", "3", "5"), length = 1, directed = TRUE),
progressions = tibble(cell_id = "a", from = "2", to = "1", percentage = 0)
)
trajectory2_rooted <- add_root(trajectory2, root_milestone_id = "5")
expect_true(all(trajectory2_rooted$milestone_network$from == c("5", "3", "4", "1")))
})
test_that("Testing add_root_using_expression",{
rooted <- add_root_using_expression(dynwrap::example_trajectory, "C")
expect_equal(
rooted$root_milestone_id,
"milestone_begin"
)
})
test_that("Testing calculate_pseudotime", {
trajectory <- add_root(trajectory)
trajectory <- add_pseudotime(trajectory)
expect_equal(trajectory$pseudotime, c("a" = 0.2, "b" = 1.6, "c" = 2.8, "d" = 4.5, "e" = 4.6, "f" = 7.0))
})
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