tests/testthat/test-symbol_conversion.R

In browaeysrobin/nichenetr: Modeling Intercellular Communication by Linking Ligands to Target Genes with NicheNet

context("Symbol conversion functions")

test_that("human-mouse and symbol-alias conversion works", {
  human_symbols = c("TNF","IFNG","IL-15","CTGF")
  aliases = human_symbols %>% convert_alias_to_symbols(organism = "human")
  expect_type(aliases,"character")

  mouse_symbols_v1 = human_symbols %>% convert_human_to_mouse_symbols() %>% .[!is.na(.)]
  expect_type(mouse_symbols_v1,"character")

  mouse_symbols_v2 = human_symbols %>% convert_human_to_mouse_symbols(version = 2) %>% .[!is.na(.)]
  expect_type(mouse_symbols_v2,"character")

  aliases_mouse = mouse_symbols_v1 %>% convert_alias_to_symbols(organism = "mouse")
  expect_type(aliases_mouse,"character")

  aliases_mouse_v2 = mouse_symbols_v2 %>% convert_alias_to_symbols(organism = "mouse")
  expect_type(aliases_mouse_v2,"character")

  human_symbols_back_v1 = mouse_symbols_v1 %>% convert_mouse_to_human_symbols(version = 1)
  expect_type(human_symbols_back_v1,"character")

  human_symbols_back_v2 = mouse_symbols_v2 %>% convert_mouse_to_human_symbols(version = 2)
  expect_type(human_symbols_back_v2,"character")

  aliases = human_symbols_back_v2 %>% convert_alias_to_symbols(organism = "human")
  expect_type(aliases,"character")
})
test_that("Seurat alias conversion works", {
  options(timeout = 3600)
  seurat_object_lite = readRDS(url("https://zenodo.org/record/3531889/files/seuratObj_test.rds"))

  seurat_object_lite2 = seurat_object_lite %>% alias_to_symbol_seurat(organism = "mouse")
  expect_equal(typeof(seurat_object_lite2), "S4")

  seurat_object_lite <- UpdateSeuratObject(seurat_object_lite)

  if (grepl("^5", packageVersion("Seurat")) & grepl("^5", seurat_object_lite@version)){
    expect_warning(alias_to_symbol_seurat(seurat_object_lite, "mouse"))
    same_seurat_obj <- suppressWarnings(alias_to_symbol_seurat(seurat_object_lite, "mouse"))
    expect_true(all(rownames(seurat_object_lite) == rownames(same_seurat_obj)))
  } else {
    seurat_object_lite2 = seurat_object_lite %>% alias_to_symbol_seurat(organism = "mouse")
    expect_equal(typeof(seurat_object_lite2), "S4")
  }

})