tests/testthat/test_deconvolution_mouse.R

In grst/immunedeconv: Methods for immune cell deconvolution

test_mat <- read_tsv("bulk_mat_mouse.tsv") %>%
  as.data.frame() %>%
  tibble::column_to_rownames("gene_symbol")

test_that("mmcp_counter works", {
  res <- deconvolute_mmcp_counter(test_mat)
  assert("matrix dimensions consistent", ncol(res) == ncol(test_mat))
})

test_that("seqimmucc works", {
  res <- deconvolute_seqimmucc(test_mat, algorithm = "LLSR")
  assert("matrix dimensions consistent", ncol(res) == ncol(test_mat))
})

test_that("DCQ works", {
  res <- deconvolute_dcq(test_mat)
  assert("matrix dimensions consistent", ncol(res) == ncol(test_mat))
})

test_that("BASE works", {
  res <- deconvolute_base_algorithm(test_mat, n_permutations = 5)
  assert("matrix dimensions consistent", ncol(res) == ncol(test_mat))
})

test_that("DCQ works without reducing cell types", {
  res <- deconvolute_dcq(test_mat, combine_cells = FALSE, n_repeats = 5)
  assert("matrix dimensions consistent", ncol(res) == ncol(test_mat))
})


test_that("generic deconvolution works for all methods", {
  lapply(deconvolution_methods_mouse, function(method) {
    print(paste0("method is ", method))
    res <- deconvolute_mouse(test_mat, method, algorithm = "LLSR")
    # matrix has the 'cell type' column -> +1
    assert("matrix dimensions consistent", ncol(res) == ncol(test_mat) + 1)
    assert("cell type column exists", colnames(res)[1] == "cell_type")
    assert("sample names consistent with input", colnames(res)[-1] == colnames(test_mat))
  })
})

# test_that("mouse gene names can be converted into their human orthologus, and vice versa", {
#   test_mat_newGenes <- convert_human_mouse_genes(test_mat[1:1000, ], convert_to = "human")
#   assert("matrix dimensions consistent", ncol(test_mat_newGenes) == ncol(test_mat))
#
#   test_mat_human <- read_tsv("bulk_mat.tsv") %>%
#     as.data.frame() %>%
#     tibble::column_to_rownames("gene_symbol")
#   test_mat_newGenes <- convert_human_mouse_genes(test_mat_human[1:1000, ], convert_to = "mouse")
#   assert("matrix dimensions consistent", ncol(test_mat_newGenes) == ncol(test_mat_human))
# })