tests/testthat/test-run-pathfindr.R

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

## Tests for core function - Aug 2023

# set up input data
input_data_frame <- example_pathfindR_input[1:10, c(1, 3)]
colnames(input_data_frame) <- c("GENE", "P_VALUE")

test_that("`run_pathfindR()` -- works as expected", {
  mock_fetch_gene_sets <- mockery::mock(list(), cycle = TRUE)
  mock_return_pin_path <- mockery::mock("/path/to/some/PIN/SIF", cycle = TRUE)
  mock_input_processing <- mockery::mock(input_data_frame, cycle = TRUE)
  mock_active_snw_enrichment_wrapper <- mockery::mock(data.frame(), c())
  mock_summarize_enrichment_results <- mockery::mock(data.frame())
  mock_annotate_term_genes <- mockery::mock(example_pathfindR_output)
  mock_plot <- mockery::mock(NULL)

  mockery::stub(run_pathfindR, "fetch_gene_sets", mock_fetch_gene_sets)
  mockery::stub(run_pathfindR, "return_pin_path", mock_return_pin_path)
  mockery::stub(run_pathfindR, "input_processing", mock_input_processing)
  mockery::stub(run_pathfindR, "active_snw_enrichment_wrapper", mock_active_snw_enrichment_wrapper)
  mockery::stub(run_pathfindR, "summarize_enrichment_results", mock_summarize_enrichment_results)
  mockery::stub(run_pathfindR, "annotate_term_genes", mock_annotate_term_genes)
  mockery::stub(run_pathfindR, "graphics::plot", mock_plot)
  mockery::stub(run_pathfindR, "create_HTML_report", NULL)

  expected_messages <- paste(
    c(
      "The input looks OK", "Plotting the enrichment bubble chart",
      paste(c(
        paste0("Found ", nrow(example_pathfindR_output), " enriched terms\n"),
        "You may run:", "- cluster_enriched_terms() for clustering enriched terms",
        "- visualize_terms() for visualizing enriched term diagrams\n"
      ), collapse = "\n")
    ),
    collapse = "|"
  )
  # wrapper functions correctly - with output_dir provided
  out_dir <- file.path(tempdir(check = TRUE), "core_test")
  expect_message(
    res <- run_pathfindR(input_data_frame, output_dir = out_dir),
    expected_messages
  )
  expect_is(res, "data.frame")
  expect_identical(res, example_pathfindR_output)
  mockery::expect_called(mock_fetch_gene_sets, 1)
  mockery::expect_called(mock_return_pin_path, 1)
  mockery::expect_called(mock_input_processing, 1)
  mockery::expect_called(mock_active_snw_enrichment_wrapper, 1)
  mockery::expect_called(mock_summarize_enrichment_results, 1)
  mockery::expect_called(mock_annotate_term_genes, 1)
  mockery::expect_called(mock_plot, 1)

  # warning raised as expected when no results found
  expect_warning(res <- run_pathfindR(input_data_frame), "Did not find any enriched terms!")
  expect_identical(res, data.frame())
})

test_that("`run_pathfindR()` argument checks work", {
  expect_error(
    run_pathfindR(input_data_frame, plot_enrichment_chart = "INVALID"),
    "`plot_enrichment_chart` should be either TRUE or FALSE"
  )
  expect_error(
    run_pathfindR(input_data_frame, list_active_snw_genes = "INVALID"),
    "`list_active_snw_genes` should be either TRUE or FALSE"
  )
})