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context("test-rename_nmf_signatures")
# Load NMF data
nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
package = "MutationalPatterns"
))
# Load signatures
signatures <- get_known_signatures()
# Run function
output <- rename_nmf_signatures(nmf_res, signatures)
# Run without a suffix
output_suffix <- rename_nmf_signatures(nmf_res, signatures, suffix = "")
# Change how similar the signatures have to be, before they are considered similar.
output_strict <- rename_nmf_signatures(nmf_res, signatures, cutoff = 0.95)
# Change the base_name of the signatures that end up with a letter name.
output_basename <- rename_nmf_signatures(nmf_res, signatures, cutoff = 0.95, base_name = "Signature_")
# Tests that nmf_res is still nmf_res
test_that("Outputs a list", {
expect_true(inherits(output, c("list")))
expect_true(inherits(output_suffix, c("list")))
expect_true(inherits(output_strict, c("list")))
expect_true(inherits(output_basename, c("list")))
})
test_that("Output contains signatures, contribution and reconstructed", {
expect_identical(names(output), c("signatures", "contribution", "reconstructed"))
expect_identical(names(output_suffix), c("signatures", "contribution", "reconstructed"))
expect_identical(names(output_strict), c("signatures", "contribution", "reconstructed"))
expect_identical(names(output_basename), c("signatures", "contribution", "reconstructed"))
})
test_that("Output elements are matrixes", {
expect_true(inherits(output$signatures, "matrix"))
expect_true(inherits(output$contribution, "matrix"))
expect_true(inherits(output$reconstructed, "matrix"))
expect_true(inherits(output_suffix$signatures, "matrix"))
expect_true(inherits(output_suffix$contribution, "matrix"))
expect_true(inherits(output_suffix$reconstructed, "matrix"))
expect_true(inherits(output_strict$signatures, "matrix"))
expect_true(inherits(output_strict$contribution, "matrix"))
expect_true(inherits(output_strict$reconstructed, "matrix"))
expect_true(inherits(output_basename$signatures, "matrix"))
expect_true(inherits(output_basename$contribution, "matrix"))
expect_true(inherits(output_basename$reconstructed, "matrix"))
})
# Test that names are correctly changed
test_that("New signature names are correct", {
expect_equal(colnames(output$signatures), c("SBS5-like", "SBS1-like"))
expect_equal(rownames(output$contribution), c("SBS5-like", "SBS1-like"))
expect_equal(colnames(output_suffix$signatures), c("SBS5", "SBS1"))
expect_equal(rownames(output_suffix$contribution), c("SBS5", "SBS1"))
expect_equal(colnames(output_strict$signatures), c("SBSA", "SBSB"))
expect_equal(rownames(output_strict$contribution), c("SBSA", "SBSB"))
expect_equal(colnames(output_basename$signatures), c("Signature_A", "Signature_B"))
expect_equal(rownames(output_basename$contribution), c("Signature_A", "Signature_B"))
})
# Test that an error is given when multiple signatures are matched to the same reference.
nmf_res2 <- nmf_res
nmf_res2$signatures[, 1] <- nmf_res2$signatures[, 2]
test_that("An error is given when multiple sigs are matched to the same ref sig", {
expect_error(
{
rename_nmf_signatures(nmf_res2, signatures)
},
"You have multiple NMF signatures that are linked to the same existing signature"
)
})
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