tests/testthat/test.genotFitness.R

In OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis

inittime <- Sys.time()
cat(paste("\n Starting genotFitness at", date(), "\n"))

test_that("Conversion for data frame", {
    (m4 <- data.frame(G = c("A, B", "A", "WT", "B"), F = c(3, 2, 1, 4)))
    fem4 <- allFitnessEffects(genotFitness = m4)
    expect_true(all(evalAllGenotypes(fem4, addwt = TRUE, order = FALSE) ==
                    m4[c(3, 2, 4, 1), ]))
})


test_that("Conversion for matrix", {

    m5 <- cbind(c(1, 0, 1, 0), c(0, 1, 1, 0), c(2, 3, 5.5, 1))
    fem5 <- allFitnessEffects(genotFitness = m5)
    evalAllGenotypes(fem5, addwt = TRUE, order = FALSE)
    expect_true(all(evalAllGenotypes(fem5, addwt = TRUE, order = FALSE)[, 2] ==
                    m5[c(4, 1, 2, 3), 3]))
    
})


test_that("Conversion for incomplete matrix", {
    m6 <- cbind(c(1, 1), c(1, 0), c(2, 3))
    fem6 <- allFitnessEffects(genotFitness = m6)
    evalAllGenotypes(fem6, addwt = TRUE, order = FALSE)
    expect_true(all(
        evalAllGenotypes(fem6, addwt = TRUE,
                         order = FALSE)[, 2]
        == c(1, m6[2, 3], 0, m6[1, 3]))) ## flfast breaking change
})


test_that("We fail with order", {
    expect_error(OncoSimulR:::from_genotype_fitness(data.frame(G = "A > B", F = 1)))
})

test_that("We fail with wrong separator, :", {
    expect_error(OncoSimulR:::from_genotype_fitness(data.frame(G = "A : B", F = 1)))
})


test_that("Dividing fitness by wt and missing genot is 1", {
    m7 <- cbind(c(1, 1, 0), c(1, 0, 0), c(2, 3, 5))
    ## No longer that message
    expect_warning(fem7 <- allFitnessEffects(genotFitness = m7),
                    "Fitness of wildtype != 1. Dividing all fitnesses by fitness of wildtype.",
                    fixed = TRUE)
    ## expect_equivalent(evalAllGenotypes(fem7, order = FALSE, addwt = TRUE)[, 2],
    ##                   c(5, 3, 0, 2))
    expect_equivalent(evalAllGenotypes(fem7, order = FALSE, addwt = TRUE)[, 2],
                      c(1, 3/5, 0, 2/5))
})

test_that("The WT is added if absent, in two cases", {
    m7 <- cbind(c(1, 1), c(1, 0), c(2, 3))
    expect_warning(fem7 <- allFitnessEffects(genotFitness = m7),
                   "No wildtype in the fitness landscape",
                   fixed = TRUE)
    ## the WT was added to the fitness landscape
    expect_identical(fem7$fitnessLandscape[, "Fitness"],
                     c(1, 2, 3))
    ag <- evalAllGenotypes(fem7, order = FALSE)
    ## internal call
    ## the wt was added to the output from allGenotypes_to_matrix
    ## though this is mostly redundant now
    expect_equivalent(OncoSimulR:::allGenotypes_to_matrix(ag)[, 3],
                      c(1, 3, 0, 2))
    ## the user visible, which is via plotFitnessLandscape -> to_Fitness_Matrix
    plot(ag)
})


test_that("genotFitness not combined with others", {

    m7 <- cbind(c(1, 1, 0), c(1, 0, 0), c(2, 3, 5))
    
    expect_error(allFitnessEffects(genotFitness = m7,
                                   noIntGenes = c(.1, .2)),
                 "You have a non-null genotFitness.",
                 fixed = TRUE)

    expect_error(allFitnessEffects(genotFitness = m7,
                                   epistasis = c("A" = .3,
                                            "B" = .1,
                                            "C" = .2)),
                 "You have a non-null genotFitness.",
                 fixed = TRUE)
    
    expect_error(allFitnessEffects(genotFitness = m7,
                                   orderEffects = c("G > H" = 1.1)),
                 "You have a non-null genotFitness.",
                 fixed = TRUE)


    p3 <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c", "f"),
                  child = c("a", "b", "d", "e", "c", "c", "f", "f", "g", "g"),
                  s = c(0.01, 0.02, 0.03, 0.04, 0.1, 0.1, 0.2, 0.2, 0.3, 0.3),
                  sh = c(rep(0, 4), c(-.9, -.9), c(-.95, -.95), c(-.99, -.99)),
                  typeDep = c(rep("--", 4), 
                              "XMPN", "XMPN", "MN", "MN", "SM", "SM"))
    
    expect_error(allFitnessEffects(rT = p3, genotFitness = m7),
                 "You have a non-null genotFitness.",
                 fixed = TRUE)
   
})


test_that("Missing genotypes defaults: WT 1, others 0", {
    (m8 <- data.frame(G = c("A, B, C", "B"), F = c(3, 2)))
    exp_m8 <- data.frame(
        Genotype = c("WT", "A", "B", "C", "A, B", "A, C",
                     "B, C", "A, B, C"),
        Fitness = c(1, 0, 2, rep(0, 4), 3),
        stringsAsFactors = FALSE)
    
    o_m8 <- evalAllGenotypes(allFitnessEffects(genotFitness = m8),
                     addwt = TRUE)
    ## as exp_m8 does not have the evalAllGenotypes attribute
    expect_equivalent(o_m8, exp_m8)

    

    (m9 <- rbind(
         c(0, 1, 1, 0, 2),
         c(1, 1, 0, 0, 4),
         c(1, 0, 1, 0, 1.5)
     ))
    
    exp_m9 <- data.frame(
        Genotype = c("WT", "A", "B", "C", "D",
                     "A, B", "A, C", "A, D", 
                     "B, C", "B, D", "C, D",
                     "A, B, C", "A, B, D", "A, C, D", "B, C, D",
                     "A, B, C, D"),
        Fitness = c(1, rep(0, 4),
                    4, 1.5, 0, 2,
                    rep(0, 7)),
        stringsAsFactors = FALSE)

    o_m9 <- evalAllGenotypes(allFitnessEffects(genotFitness = m9), addwt = TRUE)

    expect_equivalent(o_m9, exp_m9)
    
})

cat(paste("\n Ending genotFitness at", date(), "\n"))
cat(paste("  Took ", round(difftime(Sys.time(), inittime, units = "secs"), 2), "\n\n"))
rm(inittime)