tests/testthat/test-active-snw-filtering.R

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

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

example_unfiltered_snws_len <- length(example_unfiltered_snws)

test_that("`filter_active_subnetworks()` -- returns expected list object", {
  snws_filtered <- filter_active_subnetworks(active_snws = example_unfiltered_snws, sig_genes_vec = input_data_frame$GENE)
  expect_is(snws_filtered, "list")
  expect_length(snws_filtered, 2)
  expect_is(snws_filtered$subnetworks, "list")
  expect_is(snws_filtered$scores, "numeric")

  expect_is(snws_filtered$subnetworks[[1]], "character")
  expect_true(length(snws_filtered$subnetworks) <= example_unfiltered_snws_len)

  # empty file case
  empty_snws <- list()
  expect_null(suppressWarnings(filter_active_subnetworks(active_snws = empty_snws, sig_genes_vec = input_data_frame$GENE)))
})

test_that("`filter_active_subnetworks()` -- `score_quan_thr` works", {
  snws_filtered <- filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    score_quan_thr = -1, sig_gene_thr = 0
  )
  expect_length(snws_filtered$subnetworks, example_unfiltered_snws_len)

  for (q_thr in seq(0.1, 1, by = 0.1)) {
    snws_filtered <- filter_active_subnetworks(
      active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
      score_quan_thr = q_thr, sig_gene_thr = 0
    )
    exp_len <- example_unfiltered_snws_len * (1 - q_thr)
    expect_length(snws_filtered$subnetworks, as.integer(exp_len + 0.5))
  }
})

test_that("`filter_active_subnetworks()` -- `sig_gene_thr` works", {
  snws_filtered1 <- filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    sig_gene_thr = 0.02, score_quan_thr = -1
  )
  snws_filtered2 <- filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    sig_gene_thr = 0.1, score_quan_thr = -1
  )

  expect_true(length(snws_filtered2$subnetworks) < example_unfiltered_snws_len)
  expect_true(length(snws_filtered1$subnetworks) > length(snws_filtered2$subnetworks))
})

test_that("`filter_active_subnetworks()` -- argument checks work", {
  expect_error(
    filter_active_subnetworks(active_snws = example_unfiltered_snws, sig_genes_vec = list()),
    "`sig_genes_vec` should be a vector"
  )

  expect_error(filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    score_quan_thr = "INVALID"
  ), "`score_quan_thr` should be numeric")
  expect_error(filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    score_quan_thr = -2
  ), "`score_quan_thr` should be in \\[0, 1\\] or -1 \\(if not filtering\\)")
  expect_error(filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    score_quan_thr = 2
  ), "`score_quan_thr` should be in \\[0, 1\\] or -1 \\(if not filtering\\)")

  expect_error(filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    sig_gene_thr = "INVALID"
  ), "`sig_gene_thr` should be numeric")
  expect_error(filter_active_subnetworks(
    active_snws = example_unfiltered_snws, sig_genes_vec = example_pathfindR_input$Gene.symbol,
    sig_gene_thr = -1
  ), "`sig_gene_thr` should be in \\[0, 1\\]")
})