tests/testthat/test-define-paths.R

In LTLA/TrajectoryUtils: Single-Cell Trajectory Analysis Utilities

# This tests the defineMSTPaths function.
# library(testthat); library(TrajectoryUtils); source("setup.R"); source("test-define-paths.R")

library(igraph)
g <- make_graph(c("A", "B", "B", "C", "B", "D"), directed=FALSE)
solo <- simplify(make_graph(c("A", "A", "B", "B")))
empty <- make_graph(character(0))

test_that("defineMSTPaths works with preset roots", {
    paths <- defineMSTPaths(g, roots="A")
    expect_identical(paths, list(c("A", "B", "C"), c("A", "B", "D")))

    paths <- defineMSTPaths(g, roots="B")
    expect_identical(paths, list(c("B", "A"), c("B", "C"), c("B", "D")))

    # Testing for multiple components:
    g2 <- make_graph(c("A", "B", "B", "C", "B", "D", "E", "F"), directed=FALSE)
    expect_error(defineMSTPaths(g2, roots="B"), "one node")

    paths <- defineMSTPaths(g2, roots=c("D", "E"))
    expect_identical(paths, list(c("D", "B", "A"), c("D", "B", "C"), c("E", "F")))

    # Testing for singletons.
    expect_identical(defineMSTPaths(empty, roots=character(0)), list())
    expect_identical(defineMSTPaths(solo, roots=c("A", "B")), list("A", "B"))
})

test_that("defineMSTPaths works with per-node times", {
    paths <- defineMSTPaths(g, times=c(A=0, B=1, C=2, D=3))
    expect_identical(paths, list(c("A", "B", "C"), c("A", "B", "D")))

    paths <- defineMSTPaths(g, times=c(A=0, B=-1, C=2, D=3))
    expect_identical(paths, list(c("B", "A"), c("B", "C"), c("B", "D")))

    # Multiple convergent paths generated:
    paths <- defineMSTPaths(g, times=c(A=0, B=5, C=2, D=3))
    expect_identical(paths, list(c("A", "B"), c("C", "B"), c("D", "B")))

    paths <- defineMSTPaths(g, times=c(A=0, B=5, C=2, D=10))
    expect_identical(paths, list(c("A", "B", "D"), c("C", "B", "D")))
    
    # Works for ties in adjacent nodes.
    paths <- defineMSTPaths(g, times=c(A=0, B=0, C=2, D=10))
    expect_identical(paths, list("A", c("B", "C"), c("B", "D")))

    # Works for multiple components.
    g2 <- make_graph(c("A", "B", "B", "C", "B", "D", "E", "F"), directed=FALSE)
    paths <- defineMSTPaths(g2, times=c(A=0, B=1, C=2, D=3, E=10, F=0))
    expect_identical(paths, list(c("A", "B", "C"), c("A", "B", "D"), c("F", "E")))

    # Works for multiple components after adding timing directions.
    g2 <- make_graph(c("A", "B", "B", "C", "B", "D", "D", "E", "D", "F"), directed=FALSE)
    paths <- defineMSTPaths(g2, times=c(A=10, B=0, C=2, D=0, E=10, F=10))
    expect_identical(paths, list(c("B", "A"), c("B", "C"), c("D", "E"), c("D", "F")))

    # Testing for singletons.
    expect_identical(defineMSTPaths(empty, times=numeric(0), roots=character(0)), list())
    expect_identical(defineMSTPaths(solo, times=c(A=1, B=2)), list("A", "B"))
})

set.seed(1000)
test_that("per-node timings can be computed from clusters", {
    clusters <- sample(LETTERS[1:4], 100, replace=TRUE)
    timings <- runif(100)

    ref <- defineMSTPaths(g, times=vapply(split(timings, clusters), mean, 0))
    out <- defineMSTPaths(g, times=timings, cluster=clusters)
    expect_identical(ref, out)

    out <- defineMSTPaths(g, times=timings, cluster=factor2matrix(clusters))
    expect_identical(ref, out)

    ref <- defineMSTPaths(g, times=vapply(split(timings, clusters), median, 0))
    out <- defineMSTPaths(g, times=timings, cluster=clusters, use.median=TRUE)
    expect_identical(ref, out)

    out <- defineMSTPaths(g, times=timings, cluster=factor2matrix(clusters), use.median=TRUE)
    expect_identical(ref, out)
})