tests/testthat/test-viper_wrapper.R

In saezlab/dorothea_R: Collection Of Human And Mouse TF Regulons

test_that("test run_viper with matrix as input", {
  m = readRDS(
    system.file("testdata", "toy_matrix.rds", package = "dorothea")
  )
  r = dplyr::filter(dorothea_hs, confidence %in% c("A", "B"))
  res = run_viper(m, r, options =  list(method = "scale", minsize = 4,
                                        eset.filter = FALSE, verbose = FALSE))

  tidy_res = run_viper(m, r, options =  list(method = "scale", minsize = 4,
                                             eset.filter = FALSE,
                                             verbose = FALSE),
                       tidy = TRUE)

  expected_res = readRDS(
    system.file("testdata", "output_matrix.rds", package = "dorothea")
    )

  expected_res_tidy = readRDS(
    system.file("testdata", "output_matrix_tidy.rds", package = "dorothea")
  )

  expect_equal(res, expected_res)
  expect_equal(tidy_res, expected_res_tidy)
})

test_that("test run_viper with eset as input", {
  m = readRDS(
    system.file("testdata", "toy_eset.rds", package = "dorothea")
  )
  r = dplyr::filter(dorothea_hs, confidence %in% c("A", "B"))

  res = run_viper(m, r, options =  list(method = "scale", minsize = 4,
                                        eset.filter = FALSE, verbose = FALSE))

  tidy_res = run_viper(m, r, options =  list(method = "scale", minsize = 4,
                                             eset.filter = FALSE,
                                             verbose = FALSE),
                       tidy = TRUE)

  expected_res = readRDS(
    system.file("testdata", "output_eset.rds", package = "dorothea")
  )

  expected_res_tidy = readRDS(
    system.file("testdata", "output_eset_tidy.rds", package = "dorothea")
  )

  expect_equal(res, expected_res)
  expect_equal(tidy_res, expected_res_tidy)
})


test_that("test run_viper with seurat as input", {
  library(Seurat)
  m = readRDS(
    system.file("testdata", "toy_seurat.rds", package = "dorothea")
  )
  r = dplyr::filter(dorothea_hs, confidence %in% c("A", "B"))

  res = run_viper(m, r, options =  list(method = "scale", minsize = 4,
                                        eset.filter = FALSE, verbose = FALSE))

  tidy_res = run_viper(m, r, options =  list(method = "scale", minsize = 4,
                                             eset.filter = FALSE,
                                             verbose = FALSE),
                       tidy = TRUE)

  expected_res = readRDS(
    system.file("testdata", "output_seurat.rds", package = "dorothea")
  )

  expect_equal(res, expected_res)
  expect_equal(tidy_res, expected_res)

  # check raised warning when tidy is set to T
  expect_warning(
    run_viper(m, r, options = list(method = "scale", minsize = 4,
                                   eset.filter = FALSE,
                                   verbose = FALSE),
              tidy = TRUE),
    "The argument 'tidy' cannot be TRUE for Seurat objects. 'tidy' is set to FALSE")

  # Check key of seurat assays
  expect_equal(unname(Seurat::Key(res)), c("rna_","dorothea_"))

})