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fixes small bugs and updates tests
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@KrystynaGrzesiak
KrystynaGrzesiak committed Aug 28, 2024
1 parent 759f143 commit e1ba4d7
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Showing 3 changed files with 34 additions and 31 deletions.
2 changes: 1 addition & 1 deletion R/motifs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ add_motifs <- function(motifs, sequence) {

for(iter in na.omit(iterations)) {

if(length(iterations) == 1)
if(length(motifs) == 1)
motifs_grid <- data.frame(unlist(maximum_motifs_positions))
else
motifs_grid <- t(sapply(1:iter, function(i){
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12 changes: 6 additions & 6 deletions tests/testthat/test-motifs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ test_that("generate list of motifs", {

motifs <- generate_motifs(alphabet, 1, 1, n, d, weights, validate = FALSE)

expect_equal(motifs, list(c("c", "_", "_", "a", "a", "a")))
expect_equal(motifs, list(c("c", "_", "a", "_", "a")))
})

test_that("motif injection", {
Expand All @@ -81,13 +81,13 @@ test_that("motif injection", {
motifs <- generate_motifs(letters[1:4], 2, 2, 4, 2)
injected_sequence <- add_motifs(motifs, sequence)
expect_equal(injected_sequence,
structure(c("a", "c", "b", "d", "c", "c", "d", "d"),
structure(c("d", "c", "a", "c", "c", "c", "c", "d"),
motifs = list(c("d", "c"),
c("a", "c", "_", "_", "c")),
masks = list(c(FALSE, FALSE, FALSE, TRUE,
TRUE, FALSE, FALSE, FALSE),
c(TRUE, TRUE, FALSE, FALSE,
TRUE, FALSE, FALSE, FALSE))))
masks = list(c(TRUE, TRUE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE),
c(FALSE, FALSE, TRUE, TRUE, FALSE,
FALSE, TRUE, FALSE))))
})

test_that("set of motifs cannot be injected", {
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51 changes: 27 additions & 24 deletions tests/testthat/test-sequences.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,23 @@ library(testthat)

context("Sequence generation")

test_that("generate single sequence", {

test_that("generate single sequence", {
set.seed(42)
seq <- generate_sequence(5, 1L:4)
expect_equal(seq, c(1L, 1L, 1L, 1L, 2L))

motifs <- generate_motifs(1:4, 3, 1, n = 4, d = 6)
sequence <- generate_negative_sequence(5, 1L:4, motifs)
expect_equal(sequence, c(3L, 2L, 1L, 2L, 4L))
})

test_that("sequence probabilites", {
set.seed(42)
seqProbs <- runif(6)
seqProbs <- seqProbs / sum(seqProbs)

long_sequence <- generate_sequence(10e6, 1:6, seqProbs)
motifs <- generate_motifs(1:4, 3, 1, n = 4, d = 6)

long_sequence <- generate_negative_sequence(10e5, 1:6, motifs, seqProbs)
seqFreqs <- c(table(long_sequence) / length(long_sequence))
names(seqFreqs) <- NULL
expect_equal(seqProbs, c(seqFreqs), tolerance = 10e-4)
Expand Down Expand Up @@ -64,7 +69,7 @@ test_that("k-mer counts", {

kmers <- count_seq_kmers(seq_data, alph)

expect_equal(dim(kmers), c(20L, 6189L))
expect_equal(dim(kmers), c(20L, 6201L))

kmers <- count_seq_kmers(seq_data, alph, n = 1, d = 0)
expect_equal(ncol(kmers), length(alph))
Expand All @@ -87,8 +92,7 @@ test_that("k-mer data", {
kmer_data <- generate_kmer_data(n_seq, sequence_length, alph, motifs,
n_injections, fraction)


expect_equal(dim(kmer_data), c(20L, 5718L))
expect_equal(dim(kmer_data), c(20L, 5022L))
expect_equal(n_seq, nrow(kmer_data))

# correct fraction of positive sequences
Expand All @@ -113,18 +117,17 @@ test_that("Interaction model works", {
results <- generate_kmer_data(n_seq, sequence_length, alph,
motifs, n_injections = 3)
expect_identical(
c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,
1L, 1L, 0L, 0L, 0L), get_target_interactions(results)
c(1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L,
0L, 0L, 1L, 0L, 0L), get_target_interactions(results)
)

expect_equal(
c(3.2669325505849, 3.2669325505849, 0.824915252858773, 3.2669325505849,
0.824915252858773, 1.01497719204053, 0.745780731318519,
2.05459328205325, 1.16902287956327, 1.77926696231589,
-1.69982326356694, -1.69982326356694, -1.69982326356694,
-1.69982326356694, -1.69982326356694, -1.69982326356694,
-1.69982326356694, -1.69982326356694, -1.69982326356694,
-1.69982326356694), get_target_interactions(results, binary = FALSE)
c(2.3877928876318, 4.19229120924138, 2.12166230170988, 0.988599377218634,
4.47515172231942, 1.58585822791792, 1.17262414400466, 0.266789596760646,
4.73356275283732, 2.3877928876318, -1.03832712979056, -1.03832712979056,
-1.03832712979056, -1.03832712979056, -1.03832712979056, -1.03832712979056,
-1.03832712979056, -1.03832712979056, -1.03832712979056, -1.03832712979056
), get_target_interactions(results, binary = FALSE)
)
})

Expand All @@ -141,12 +144,12 @@ test_that("Additive model works", {
results <- generate_kmer_data(n_seq, sequence_length, alph,
motifs, n_injections = 3)
expect_identical(
c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L,
0L, 0L, 0L, 0L, 1L), get_target_additive(results)
c(0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 0L,
0L, 1L, 0L, 0L, 0L), get_target_additive(results)
)

expect_equal(
c(2.05890567833558, 2.05890567833558, 0.39565183990635),
c(0.675145752727985, 1.19026312511414, 1.00235199206509),
get_target_additive(results, binary = FALSE)[1:3]
)

Expand All @@ -168,13 +171,13 @@ test_that("Logic model works", {
results <- generate_kmer_data(n_seq, sequence_length, alph,
motifs, n_injections = 3)
expect_identical(
c(0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,
1L, 0L, 0L, 0L, 1L), get_target_logic(results)
c(1L, 0L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L), get_target_logic(results)
)

expect_equal(
c(0.854367734864354, 0.854367734864354, 0.854367734864354,
0.854367734864354), get_target_logic(results, binary = FALSE)[1:4]
c(0.583639514865354, 1.4445967883803, 1.4445967883803, 0.583639514865354
), get_target_logic(results, binary = FALSE)[1:4]
)

expressions = matrix(rbinom(n_seq*2, 1, .5), nrow = n_seq)
Expand All @@ -185,7 +188,7 @@ test_that("Logic model works", {
)

expect_identical(
c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L,
c(0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 0L,
0L, 0L, 0L, 0L, 0L),
get_target_logic(results, expressions = expressions, weights = c(1, 2))
)
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