tests/testthat/test-s4_analysis_functs_1.R

In timothy-barry/sceptre: Analysis of Single-Cell CRISPR Screen Data

# most of the content of `import_data` is subfunctions
# which are tested elsewhere
test_that("import_data", {
  set.seed(12321)
  num_cells <- 29
  num_responses <- 17
  grna_target_data_frame <- make_mock_grna_target_data(c(1, 3, 1), 1, 1, 6)
  grna_matrix <- matrix(rpois(nrow(grna_target_data_frame) * num_cells, 1), ncol = num_cells) |>
    `rownames<-`(grna_target_data_frame$grna_id) |>
    set_matrix_accessibility()
  response_matrix <- matrix(rpois(num_responses * num_cells, 1), ncol = num_cells) |>
    as("TsparseMatrix")
  extra_covariates <- data.frame(x = rep("aaa", num_cells))

  sceptre_object_low_no_ec_with_response_names <- import_data(
    response_matrix = response_matrix,
    grna_matrix = grna_matrix,
    grna_target_data_frame = grna_target_data_frame,
    moi = "low",
    response_names = paste0("rrr", 1:num_responses)
  )
  sceptre_object_high_with_ec <- import_data(
    response_matrix = response_matrix,
    grna_matrix = grna_matrix,
    grna_target_data_frame = grna_target_data_frame,
    moi = "high",
    extra_covariates = extra_covariates
  )

  # most of the slots are so simple that only cursory tests are done, mostly to confirm
  # that future changes do not change the API
  all_slots <- c(
    "response_matrix", "grna_matrix", "covariate_data_frame", "covariate_matrix",
    "grna_target_data_frame", "low_moi", "covariate_names", "discovery_pairs",
    "positive_control_pairs", "formula_object", "side_code", "resampling_approximation",
    "control_group_complement", "run_permutations", "n_nonzero_trt_thresh",
    "n_nonzero_cntrl_thresh", "B1", "B2", "B3", "grna_integration_strategy",
    "grna_assignment_method", "grna_assignment_hyperparameters", "multiple_testing_alpha",
    "multiple_testing_method", "cell_removal_metrics", "cellwise_qc_thresholds",
    "mitochondrial_gene", "M_matrix", "n_nonzero_tot_vector", "discovery_pairs_with_info",
    "positive_control_pairs_with_info", "negative_control_pairs", "initial_grna_assignment_list",
    "grna_assignments_raw", "grna_assignments", "grnas_per_cell", "cells_w_zero_or_twoplus_grnas",
    "cells_in_use", "n_discovery_pairs", "n_ok_discovery_pairs", "n_positive_control_pairs",
    "n_ok_positive_control_pairs", "calibration_group_size", "n_calibration_pairs",
    "import_grna_assignment_info", "mean_cells_per_grna", "response_precomputations",
    "last_function_called", "functs_called", "calibration_result", "power_result",
    "discovery_result", "nuclear", "nf_pipeline", "integer_id", "elements_to_analyze"
  )
  expect_equal(slotNames(sceptre_object_low_no_ec_with_response_names), all_slots)
  expect_equal(slotNames(sceptre_object_high_with_ec), all_slots)

  ##### slots set in section 4 of `import_data`
  expect_equal(get_response_matrix(sceptre_object_high_with_ec), set_matrix_accessibility(response_matrix))
  expect_equal(get_grna_matrix(sceptre_object_high_with_ec), set_matrix_accessibility(grna_matrix))

  expect_true(sceptre_object_low_no_ec_with_response_names@low_moi)
  expect_false(sceptre_object_high_with_ec@low_moi)

  expect_equal(
    sceptre_object_low_no_ec_with_response_names@covariate_data_frame |> rownames(),
    as.character(seq_len(num_cells))
  )

  expect_equal(
    names(sceptre_object_low_no_ec_with_response_names@covariate_data_frame),
    c("response_n_nonzero", "response_n_umis", "grna_n_nonzero", "grna_n_umis")
  )
  expect_equal(
    names(sceptre_object_high_with_ec@covariate_data_frame),
    c("response_n_nonzero", "response_n_umis", "grna_n_nonzero", "grna_n_umis", "x")
  )
  expect_equal(
    sceptre_object_high_with_ec@covariate_data_frame$x,
    extra_covariates$x
  )

  ##### slots set in section 5 of `import_data`
  expect_equal(sceptre_object_high_with_ec@last_function_called, "import_data")
  expect_equal(names(sceptre_object_high_with_ec@functs_called), c(
    "import_data", "set_analysis_parameters",
    "assign_grnas", "run_qc", "run_calibration_check",
    "run_power_check", "run_discovery_analysis"
  ))
  expect_equal(sceptre_object_high_with_ec@functs_called |> as.logical(), rep(c(TRUE, FALSE), c(1, 6)))
})


## this function is still under construction
# TODO
# - check_set_analysis_parameters
# - reset_response_precomps and caching
# - update_dfs_based_on_grouping_strategy

test_that("set_analysis_parameters", {
  set.seed(12333)
  grna_target_data_frame <- make_mock_grna_target_data(
    num_guides_per_target = c(1, 4, 7), chr_distances = 1, chr_starts = 1,
    num_nt_guides = 5
  )
  num_cells <- 23
  num_responses <- 18
  num_targets <- nrow(grna_target_data_frame)
  response_matrix <- make_mock_response_matrices(num_responses, num_cells, patterns = "column")
  grna_matrix <- make_mock_grna_matrices(
    grna_target_data_frame, num_cells,
    non_nt_patterns = "column", nt_patterns = "row"
  )

  disc_pairs_empty <- matrix("", 0, 2) |>
    as.data.frame() |>
    setNames(c("grna_target", "response_id"))

  sceptre_object_post_all_defaults_low_moi <- import_data(
    response_matrix = response_matrix,
    grna_matrix = grna_matrix,
    grna_target_data_frame = grna_target_data_frame,
    extra_covariates = data.frame(),
    moi = "low"
  ) |>
    set_analysis_parameters(
      discovery_pairs = disc_pairs_empty
    )

  sceptre_object_post_all_defaults_high_moi <- import_data(
    response_matrix = response_matrix,
    grna_matrix = grna_matrix,
    grna_target_data_frame = grna_target_data_frame,
    moi = "high"
  ) |>
    set_analysis_parameters(
      discovery_pairs = disc_pairs_empty,
    )

  ## 0. if we call `set_analysis_parameters` again on the results nothing should change
  expect_equal(
    sceptre_object_post_all_defaults_low_moi,
    sceptre_object_post_all_defaults_low_moi |>
      set_analysis_parameters(discovery_pairs = disc_pairs_empty)
  )

  ## 1. do default values get set correctly based on MOI?

  # complement should be TRUE for high MOI and FALSE for low
  expect_true(sceptre_object_post_all_defaults_high_moi@control_group_complement)
  expect_false(sceptre_object_post_all_defaults_low_moi@control_group_complement)

  # permutations should be used for low MOI and CRT for high
  expect_false(sceptre_object_post_all_defaults_high_moi@run_permutations)
  expect_true(sceptre_object_post_all_defaults_low_moi@run_permutations)


  ## 2. does the formula behave correctly?
  expect_equal(
    as.character(sceptre_object_post_all_defaults_high_moi@formula_object)[2],
    "log(response_n_nonzero + 1) + log(response_n_umis + 1) + log(grna_n_nonzero) + log(grna_n_umis)"
  )
  sceptre_object_nonsense_formula <- import_data(
    response_matrix = response_matrix,
    grna_matrix = grna_matrix,
    grna_target_data_frame = grna_target_data_frame,
    extra_covariates = data.frame(aaa = rnorm(num_cells)), # needed for the formula
    moi = "low"
  ) |>
    set_analysis_parameters(
      discovery_pairs = disc_pairs_empty,
      formula_object = formula("~ aaa")
    )
  expect_equal(
    as.character(sceptre_object_nonsense_formula@formula_object)[2],
    "aaa"
  )

})