tests/testthat/test-import.R

In igordot/scooter: Streamlined scRNA-Seq Analysis Pipeline

test_that("import_mtx can read in 10x data", {
  counts <- import_mtx(
    data_path = system.file("extdata",
      "outs/filtered_feature_bc_matrix",
      package = "scooter"
    ),
    gene_column = 2
  )
  truth <- readRDS(system.file("extdata",
    "import_matrix_counts.rds",
    package = "scooter"
  ))
  expect_identical(counts, truth)
})

test_that("load_sample_counts_matrix can read in 10x data", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata",
      "",
      package = "scooter"
    )
  )
  expect_identical(names(counts), c("Antibody Capture", "Gene Expression"))
})

test_that("load_sample_counts_matrix can read in tsv Antibody Capture file", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "HTO.tsv",
      package = "scooter"
    )
  )
  expect_identical(rownames(counts$`Antibody Capture`), c("Hashtag1", "Hashtag2"))
})

test_that("scooter will error is there is no valid path", {
  expect_error(load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata-test", "",
      package = "scooter"
    )
  ))
})

test_that("scooter will error is there is no mtx in directory", {
  expect_error(load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("R", "",
      package = "scooter"
    )
  ))
})

test_that("load_sample_counts_matrix can read in csv Antibody Capture file", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata",
      "HTO.csv",
      package = "scooter"
    )
  )
  expect_identical(names(counts), c("Antibody Capture"))
})

test_that("scooter will remove -1 from barcodes from txt file", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata",
      "pbmc.txt",
      package = "scooter"
    )
  )
  expect_that(colnames(counts$`Gene Expression`)[1], equals("test:GGAATCTGCTTAGG"))
})

test_that("Seurat object can be created from RNA data", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  s_obj <- create_seurat_obj(
    counts_matrix = counts$`Gene Expression`,
    assay = "RNA", log_file = NULL
  )
  # only 462 genes are above zero in the test data
  expect_s4_class(s_obj, "Seurat")
})

test_that("Seurat object can be created from ADT data", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  s_obj <- create_seurat_obj(
    counts_matrix = counts$`Antibody Capture`,
    assay = "ADT", log_file = NULL
  )
  expect_s4_class(s_obj, "Seurat")
})

test_that("Seurat obj can be created", {
  pbmc_mat <- get_test_counts_matrix()
  pbmc_obj <- create_seurat_obj(counts_matrix = pbmc_mat)
  expect_s4_class(pbmc_obj, "Seurat")
})

test_that("Assay can be added to Seurat object", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  s_obj <- create_seurat_obj(
    counts_matrix = counts$`Gene Expression`,
    assay = "RNA", log_file = NULL
  )
  s_obj <- add_seurat_assay(
    seurat_obj = s_obj,
    assay = "ADT",
    counts_matrix = counts$`Antibody Capture`,
    log_file = NULL
  )
  expect_s4_class(s_obj, "Seurat")
})

test_that("Assay cannot be added to a random object", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  expect_error(add_seurat_assay(
    seurat_obj = counts,
    assay = "ADT",
    counts_matrix = counts$`Antibody Capture`,
    log_file = NULL
  ))
})

test_that("Seurat object can be filtered", {
  pbmc_mat <- get_test_counts_matrix()
  pbmc_obj <- create_seurat_obj(counts_matrix = pbmc_mat)
  pbmc_obj <- filter_data(pbmc_obj,
    log_file = NULL,
    min_genes = NULL, max_genes = NULL, max_mt = 10
  )
  expect_lt(ncol(pbmc_obj), 60)
})

test_that("Seurat object can be filtered", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  s_obj <- create_seurat_obj(
    counts_matrix = counts$`Gene Expression`,
    assay = "RNA", log_file = NULL
  )
  s_obj <- add_seurat_assay(
    seurat_obj = s_obj,
    assay = "ADT",
    counts_matrix = counts$`Antibody Capture`,
    log_file = NULL
  )
  s_obj_filt <- filter_data(
    data = s_obj,
    log_file = NULL,
    min_genes = NULL,
    max_genes = NULL,
    max_mt = 10
  )
  expect_lt(ncol(s_obj_filt), ncol(s_obj))
})

test_that("Seurat object can be log normalized", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  s_obj <- create_seurat_obj(
    counts_matrix = counts$`Gene Expression`,
    assay = "RNA", log_file = NULL
  )
  s_obj <- add_seurat_assay(
    seurat_obj = s_obj,
    assay = "ADT",
    counts_matrix = counts$`Antibody Capture`,
    log_file = NULL
  )
  s_obj_filt <- filter_data(
    data = s_obj,
    log_file = NULL,
    min_genes = NULL,
    max_genes = NULL,
    max_mt = 10
  )
  s_obj_norm <- normalize_data(
    data = s_obj_filt,
    method = "log",
    assay = "RNA"
  )
  expect_gt(ncol(s_obj_norm@assays$RNA@scale.data), 180)
})

test_that("Seurat object can be SC transform", {
  counts <- load_sample_counts_matrix(
    sample_name = "test",
    path = system.file("extdata", "",
      package = "scooter"
    )
  )
  s_obj <- create_seurat_obj(
    counts_matrix = counts$`Gene Expression`,
    assay = "RNA", log_file = NULL
  )
  s_obj <- add_seurat_assay(
    seurat_obj = s_obj,
    assay = "ADT",
    counts_matrix = counts$`Antibody Capture`,
    log_file = NULL
  )
  s_obj_filt <- filter_data(
    data = s_obj,
    log_file = NULL,
    min_genes = NULL,
    max_genes = NULL,
    max_mt = 10
  )
  s_obj_norm <- normalize_data(
    data = s_obj_filt,
    method = "sct",
    assay = "RNA"
  )
  expect_gt(ncol(s_obj_norm@assays$SCT@scale.data), 180)
})