tests/testthat/test-collapse_intron_counts.R

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

intron_mat <- Matrix::Matrix(
  data = c(
    1.0, 1, 3, 100, 10,
    2, 1, 100, 0, 10
  ),
  ncol = 2,
  sparse = TRUE
)
rownames(intron_mat) <- c("a", "a-I", "b", "b-I", "c")

usa_mat <- Matrix::Matrix(
  data = c(
    0, 1, 1, 2, 100, 1, 10,
    1, 1, 1, 80, 0, 20, 10
  ),
  ncol = 2,
  sparse = TRUE
)
rownames(usa_mat) <- c("a", "a-U", "a-A", "b", "b-U", "b-A", "c")

spliced_mat <- Matrix::Matrix(
  data = c(
    1, 3, 10,
    2, 100, 10
  ),
  ncol = 2,
  sparse = TRUE
)
rownames(spliced_mat) <- c("a", "b", "c")

unspliced_mat <- Matrix::Matrix(
  data = c(
    2, 103, 10,
    3, 100, 10
  ),
  ncol = 2,
  sparse = TRUE
)
rownames(unspliced_mat) <- c("a", "b", "c")

# We are checking only contents & names, because
# aggregate.Matrix used internally may add additional attributes

test_that("Check spliced collapse", {
  collapsed_mat <- collapse_intron_counts(intron_mat)
  collapsed_usa <- collapse_intron_counts(usa_mat)
  # check the contents
  expect_equal(
    collapsed_mat@x,
    spliced_mat@x
  )
  # check the dimnames
  expect_equal(
    collapsed_mat@Dimnames,
    spliced_mat@Dimnames
  )
  # same checks for usa mode
  expect_equal(
    collapsed_usa@x,
    spliced_mat@x
  )
  expect_equal(
    collapsed_usa@Dimnames,
    spliced_mat@Dimnames
  )
})

test_that("Check total(unspliced) collapse", {
  collapsed_mat <- collapse_intron_counts(intron_mat, "total")
  collapsed_usa <- collapse_intron_counts(usa_mat, "total")
  # check the contents
  expect_equal(
    collapsed_mat@x,
    unspliced_mat@x
  )
  # check the dimnames
  expect_equal(
    collapsed_mat@Dimnames,
    unspliced_mat@Dimnames
  )
  # same checks for usa mode
  expect_equal(
    collapsed_usa@x,
    unspliced_mat@x
  )
  expect_equal(
    collapsed_usa@Dimnames,
    unspliced_mat@Dimnames
  )
})