tests/testthat/test-clonal-family.R

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

data(bcrdata)
test_bcr_data <- bcrdata$data %>% top(1000)
test_input <- test_bcr_data %>%
  seqCluster(seqDist(test_bcr_data), .fixed_threshold = 3) %>%
  repGermline(.threads = 1) %>%
  repAlignLineage(.min_lineage_sequences = 2, .prepare_threads = 1, .align_threads = 1) %>%
  suppressWarnings()

positive_test_cases <- list(
  "Not empty result" = list(
    args = list(
      .data = test_input,
      .threads = 1
    ),
    assert_function = function(result) {
      expect_equal(immunarch:::has_no_data(result), FALSE)
      expect_equal(nrow(result[["full_clones"]]) > 0, TRUE)
    }
  ),
  "Multiple threads" = list(
    args = list(
      .data = test_input,
      .threads = 8
    ),
    assert_function = function(result) {
      expect_equal(immunarch:::has_no_data(result), FALSE)
      expect_equal(nrow(result[["full_clones"]]) > 0, TRUE)
    }
  ),
  "Dataframe only" = list(
    args = list(
      .data = test_input[["full_clones"]],
      .threads = 1
    ),
    assert_function = function(result) {
      expect_equal(immunarch:::has_no_data(result), FALSE)
      expect_equal(nrow(result) > 0, TRUE)
    }
  ),
  "Vis groups" = list(
    args = list(
      .data = test_input,
      .vis_groups = {
        clone_ids <- test_input[["full_clones"]] %>%
          unnest("Sequences") %>%
          extract2("Clone.ID")
        list(
          Group1 = clone_ids[1],
          Group2 = clone_ids[3],
          Group3 = list(clone_ids[5], clone_ids[2]),
          Group4 = c(clone_ids[7], clone_ids[4])
        )
      },
      .threads = 1
    ),
    assert_function = function(result) {
      types <- result[["full_clones"]] %>%
        unnest("TreeStats") %>%
        extract2("Type")
      # check that correct number of clonotypes is assigned to each group
      expect_equal(tabulate(match(types, "Group1")), 1)
      expect_equal(tabulate(match(types, "Group2")), 1)
      expect_equal(tabulate(match(types, "Group3")), 2)
      expect_equal(tabulate(match(types, "Group4")), 2)
    }
  )
)

for (i in seq_along(positive_test_cases)) {
  # Arrange
  test_name <- names(positive_test_cases)[i]
  args <- positive_test_cases[[i]][["args"]]
  assert_function <- positive_test_cases[[i]][["assert_function"]]

  # Act
  result <- do.call(repClonalFamily, args)

  # Assert
  test_that(
    test_name,
    assert_function(result)
  )
}

negative_test_cases <- list(
  "List of lists" = list(
    args = list(
      .data = bcrdata
    )
  ),
  "Missing columns" = list(
    args = list(
      .data = test_bcr_data[["full_clones"]],
      .threads = 1
    )
  ),
  "Missing Alignment column" = list(
    args = list(
      .data = subset(test_input[["full_clones"]], select = -c(get("Alignment"))),
      .threads = 1
    )
  )
)

for (i in seq_along(negative_test_cases)) {
  # Arrange
  test_name <- names(negative_test_cases)[i]
  args <- negative_test_cases[[i]][["args"]]

  # Act, Assert
  test_that(
    test_name,
    expect_error(do.call(repClonalFamily, args))
  )
}