tests/testthat/test_types.R

In rnabioco/valr: Genome Interval Arithmetic

genome <- read_genome(valr_example("hg19.chrom.sizes.gz"))

x <- read_bed(valr_example("6fields.bed.gz"))
x_facs <- x

x_facs$chrom <- factor(x_facs$chrom)
x_facs$strand <- factor(x_facs$strand)

x_grpd <- dplyr::group_by(x, strand)
x_facs_grpd <- dplyr::group_by(x_facs, strand)

test_that("factor types for groups are handled the same as character", {
  res_x <- bed_intersect(x_grpd, x_grpd)
  # throws 2 warnings
  expect_warning(expect_warning(res_xfacs <- bed_intersect(x_facs_grpd, x_facs_grpd)))
  expect_true(all(res_xfacs == res_x))
})


test_that("mixing factor and character vectors for grouping works", {
  res_x <- bed_intersect(x_grpd, x_grpd)
  expect_warning(bed_intersect(x_grpd, x_facs_grpd))
  res_mixed <- suppressWarnings(bed_intersect(x_grpd, x_facs_grpd))
  expect_true(all(res_x == res_mixed))
})


test_that("factors with no entries are handled ", {
  x_empty_groups <- x_facs_grpd |>
    filter(strand == "+", chrom == "chr1") |>
    group_by(strand)

  # throws 2 warnings
  expect_warning(expect_warning(bed_intersect(x_facs_grpd, x_empty_groups)))
  res_x <- suppressWarnings(bed_intersect(x_facs_grpd, x_empty_groups))
  expect_true(all(res_x$chrom == "chr1"))
  expect_true(all(res_x$strand.x == "+" & res_x$strand.y == "+"))
})

test_that("complex, raw, and other types are not supported", {
  tmp <- x
  tmp$complex <- 1 + 2i
  expect_error(bed_intersect(tmp, tmp))

  tmp <- x
  tmp$raw <- as.raw(42)
  expect_error(bed_intersect(tmp, tmp))
})

test_that("list columns are supported", {
  x$lst_col <- list(1:10)
  res <- bed_intersect(x, x)
  expect_equal(nrow(res), 16)
})

test_that("input factor columns that are not grouped are preserved in output #360", {
  x <- tibble(
    chrom = rep("chr1", 100),
    start = 0:99,
    end = 1:100,
    grps = factor(rep(LETTERS[1:10], times = 10))
  )
  y <- tibble(
    chrom = "chr1",
    start = 1,
    end = 5
  )
  res <- bed_intersect(x, y)

  expect_true(is.factor(res$grps.x))

  # levels are the same as input
  expect_true(all(levels(res$grps.x) == LETTERS[1:10]))

  # characters work as expected
  x$grps <- as.character(x$grps)
  res <- bed_intersect(x, y)
  expect_true(is.character(res$grps.x))
})