tests/testthat/test-generate_qc_report.R

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

set.seed(1665)
sce <- sim_sce(n_cells = 100, n_genes = 200, n_empty = 10)
filt_sce <- filter_counts(sce)

test_that("generating a qc report works", {
  qc_file <- generate_qc_report(
    library_id = "TEST",
    unfiltered_sce = sce,
    filtered_sce = filt_sce
  )
  expect_true(file.exists(qc_file))
  # clean up
  file.remove(qc_file)
})

test_that("generating a qc report works with a different template", {
  qc_file <- generate_qc_report(
    library_id = "TEST",
    unfiltered_sce = sce,
    filtered_sce = filt_sce,
    report_template = "test_report.Rmd"
  )
  expect_true(file.exists(qc_file))
  # clean up
  file.remove(qc_file)
})


test_that("generating a qc report fails with a missing template", {
  expect_error(generate_qc_report(
    library_id = "TEST",
    unfiltered_sce = sce,
    filtered_sce = filt_sce,
    report_template = "missing.rmd"
  ))
})