tests/testthat/test-clustering.R

In shahcompbio/signals: Single Cell Genomes with Allele Specificity

library(ggplot2)
loherror <- 0.02
nclones <- 4
clones_dist <- c(20, 15, 35, 10)
sim_data_bb <- simulate_data_cohort(
  clone_num = clones_dist,
  clonal_events = list(list("1" = c(3, 0), "5" = c(3, 1), "6" = c(3, 1)),
    list("2" = c(6, 3), "3" = c(1, 0), "6" = c(1, 0)),
    list("17" = c(3, 1), "8" = c(6, 2), "19" = c(5, 1)),
    list("4" = c(5, 2), "9" = c(4, 1)),
    "2" = c(3, 1)
  ), # opposite LOH on chr 1
  loherror = loherror,
  coverage = 30,
  rho = 0.02,
  likelihood = "betabinomial",
  nchr = 0
)

cl_state <- umap_clustering(sim_data_bb$CNbins, field = "copy", minPts = 5)
cl_bps <- umap_clustering_breakpoints(sim_data_bb$CNbins,
  minPts = 5,
  internalonly = FALSE, use_state = TRUE,
  state_remove = 2, n_neighbors = 10, fixjitter = FALSE
)
plot1 <- plot_umap(cl_state$clustering)

test_that("Test umap clustering with bin states", {
  expect_equal(length(unique(cl_state$clustering$clone_id)), 4)
  expect_true(all(table(cl_state$clustering$clone_id) %in% clones_dist))
  expect_true(is.ggplot(plot1))
})

test_that("Test umap clustering with breakpoints matrix", {
  expect_equal(length(unique(cl_bps$clustering$clone_id)), 4)
  expect_true(all(table(cl_bps$clustering$clone_id) %in% clones_dist))
})