tests/testthat/test-vaf.R

In heavywatal/rtumopp: R interface to tumopp, a tumor growth simulator in C++

test_that("make_vaf works", {
  result = tumopp("--seed=42 -N256 -k1e6")
  population = result$population[[1L]]
  extant = filter_extant(population)
  graph = make_igraph(population)
  nsam = 4L
  ncell = 4L
  .colnames = c("x", "y", "z", "id")
  expect_named(
    {
      regions = sample_uniform_regions(extant, nsam = nsam, ncell = ncell)
    },
    .colnames
  )
  .colnames = c("site", "sample", "frequency")
  expect_named(
    {
      vaf_tidy = make_longer_vaf(graph, regions$id, mu = 1)
    },
    .colnames
  )
  expect_silent({
    subgraph = subtree(graph, unlist(regions$id))
  })
  expect_silent({
    df_distances = pairwise_distances(subgraph, regions)
  })
  expect_named(df_distances, c("i", "j", "euclidean", "fst"))
  expect_identical(nrow(df_distances), as.integer(choose(nsam, 2L)))
  expect_identical(df_distances, pairwise_distances(graph, regions))
  expect_type(internal_nodes(subgraph, unlist(regions$id), sensitivity = 0.10), "integer")
})