inittime <- Sys.time()
cat(paste("\n Starting accessible_genotypes at", date(), "\n"))
test_that("We obtain same accessible genotypes with different functions plus genot_to_adjm_mat", {
## More likely to catch bugs if many iters, rather than large matrices
niter <- 100
for(i in 1:niter) {
## cat("\n i iteration fast accessible comp ", i)
for(ng in 2:6) {
rtmp <- rfitness(ng)
ajm <- OncoSimulR:::genot_to_adj_mat(rtmp)
ajmr <- OncoSimulR:::genot_to_adj_mat_R(rtmp)
expect_equal(ajm, ajmr)
a1 <- OncoSimulR:::faster_accessible_genotypes_R(rtmp, 0)
a2 <- colnames(OncoSimulR:::filter_inaccessible(ajm, 0))
a3 <- OncoSimulR:::wrap_accessibleGenotypes(rtmp, 0)
a4 <- OncoSimulR:::wrap_accessibleGenotypes_former(rtmp, 0)
expect_identical(as.integer(a1), a3)
expect_identical(as.integer(a2), a3)
expect_true(all(a3 == a4))
}
}
})
test_that("The indices of accessible genotypes are correct", {
## Make sure we do not assume matrix is ordered
mf1 <- rbind(c(0, 0, 1),
c(1, 0, 4),
c(0, 1, .2),
c(1, 1, 3))
expect_equal(OncoSimulR:::wrap_accessibleGenotypes(mf1, 0),
c(1, 2))
mf2 <- rbind(c(0, 0, 1),
c(1, 0, 4),
c(0, 1, .2),
c(1, 1, 5))
expect_equal(OncoSimulR:::wrap_accessibleGenotypes(mf2, 0),
c(1, 2, 4))
mf1 <- rbind(c(0, 0, 1),
c(0, 1, .2),
c(1, 0, 4),
c(1, 1, 3))
expect_equal(OncoSimulR:::wrap_accessibleGenotypes(mf1, 0),
c(1, 3))
mf2 <- rbind(
c(0, 1, .2),
c(0, 0, 1),
c(1, 0, 4),
c(1, 1, 5)
)
expect_equal(OncoSimulR:::wrap_accessibleGenotypes(mf2, 0),
c(2, 3, 4))
mf2 <- rbind(
c(0, 1, .2),
c(0, 0, 1),
c(1, 1, 5),
c(1, 0, 4)
)
expect_equal(OncoSimulR:::wrap_accessibleGenotypes(mf2, 0),
c(2, 3, 4))
mf2 <- rbind(
c(0, 1, .2),
c(0, 0, 1),
c(1, 1, 5),
c(1, 0, .4)
)
expect_equal(OncoSimulR:::wrap_accessibleGenotypes(mf2, 0),
c(2))
})
test_that("The indices of adjancey matrices are correct", {
## Make sure we do not assume matrix is ordered
trueam <- matrix(NA, nrow = 4, ncol = 4)
trueam[1, 2] <- 3
trueam[1, 3] <- -0.8
trueam[2, 4] <- -1
trueam[3, 4] <- 2.8
colnames(trueam) <- rownames(trueam) <- 1:4
mf1 <- rbind(c(0, 0, 1),
c(1, 0, 4),
c(0, 1, .2),
c(1, 1, 3))
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf1),
OncoSimulR:::genot_to_adj_mat_R(mf1)))
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf1),
trueam[1:4, 1:4]))
## these two make use of the fact that we are forced to reorder some
mf2 <- mf1[c(2, 1, 4, 3), ]
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
OncoSimulR:::genot_to_adj_mat_R(mf2)))
trueam2 <- trueam
colnames(trueam2) <- rownames(trueam2) <- colnames(trueam)[c(2, 1, 4, 3)]
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
trueam2))
## ## this is potentially confusing. See below for much cleaner
## ## which compares matrices ordered by their names
## mf2 <- mf1[c(3, 1, 4, 2), ]
## expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
## OncoSimulR:::genot_to_adj_mat_R(mf2)))
## trueam2 <- trueam[c(1, 3, 2, 4), c(1, 3, 2, 4)]
## colnames(trueam2) <- rownames(trueam2) <- c(2, 1, 4, 3)
## expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
## trueam2))
## the next are cleaner: I compare the matrices ordered by the new names
ii <- c(2, 1, 4, 3)
mf2 <- mf1[ii, ]
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
OncoSimulR:::genot_to_adj_mat_R(mf2)))
trueam2 <- trueam[ii, ii]
colnames(trueam2) <- rownames(trueam2) <- 1:nrow(trueam2)
ogammf2 <- OncoSimulR:::genot_to_adj_mat(mf2)
ogammf2 <- ogammf2[order(colnames(ogammf2)), order(colnames(ogammf2))]
expect_true(all.equal(ogammf2, trueam2))
expect_true(sum(ogammf2 == trueam2, na.rm = TRUE) == 4)
expect_false(all(colnames(OncoSimulR:::genot_to_adj_mat(mf2)) == colnames(trueam)))
expect_false(sum(ogammf2 == trueam, na.rm = TRUE) == 4) ## because 2 and 3 are flipped
ii <- c(3, 1, 2, 4)
mf2 <- mf1[ii, ]
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
OncoSimulR:::genot_to_adj_mat_R(mf2)))
trueam2 <- trueam[ii, ii]
colnames(trueam2) <- rownames(trueam2) <- 1:nrow(trueam2)
ogammf2 <- OncoSimulR:::genot_to_adj_mat(mf2)
ogammf2 <- ogammf2[order(colnames(ogammf2)), order(colnames(ogammf2))]
expect_true(all.equal(ogammf2, trueam2))
expect_true(sum(ogammf2 == trueam2, na.rm = TRUE) == 4)
expect_false(all(colnames(OncoSimulR:::genot_to_adj_mat(mf2)) == colnames(trueam)))
expect_false(sum(ogammf2 == trueam, na.rm = TRUE) == 4) ## because 2 and 3 are flipped
ii <- c(1, 3, 2, 4)
mf2 <- mf1[ii, ]
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
OncoSimulR:::genot_to_adj_mat_R(mf2)))
trueam2 <- trueam[ii, ii]
colnames(trueam2) <- rownames(trueam2) <- 1:nrow(trueam2)
ogammf2 <- OncoSimulR:::genot_to_adj_mat(mf2)
ogammf2 <- ogammf2[order(colnames(ogammf2)), order(colnames(ogammf2))]
expect_true(all.equal(ogammf2, trueam2))
expect_true(sum(ogammf2 == trueam2, na.rm = TRUE) == 4)
## note this
expect_true(all(colnames(OncoSimulR:::genot_to_adj_mat(mf2)) == colnames(trueam)))
expect_false(sum(ogammf2 == trueam, na.rm = TRUE) == 4) ## because 2 and 3 are flipped
ii <- c(4, 3, 1, 2)
mf2 <- mf1[ii, ]
expect_true(all.equal(OncoSimulR:::genot_to_adj_mat(mf2),
OncoSimulR:::genot_to_adj_mat_R(mf2)))
trueam2 <- trueam[ii, ii]
colnames(trueam2) <- rownames(trueam2) <- 1:nrow(trueam2)
ogammf2 <- OncoSimulR:::genot_to_adj_mat(mf2)
ogammf2 <- ogammf2[order(colnames(ogammf2)), order(colnames(ogammf2))]
expect_true(all.equal(ogammf2, trueam2))
expect_true(sum(ogammf2 == trueam2, na.rm = TRUE) == 4)
expect_false(all(colnames(OncoSimulR:::genot_to_adj_mat(mf2)) == colnames(trueam)))
expect_false(sum(ogammf2 == trueam, na.rm = TRUE) == 4) ## because 2 and 3 are flipped
})
## For peaks, see code in test.plotFitnessLandscape.R
cat(paste("\n Ending accessible_genotypes at", date(), "\n"))
cat(paste(" Took ", round(difftime(Sys.time(), inittime, units = "secs"), 2), "\n\n"))
rm(inittime)
