tests/testthat/test_methods.R

In umap: Uniform Manifold Approximation and Projection

# tests for selecting methods

i.select <- c(1:12, 61:72, 121:132)
i4 <- iris[i.select,
           c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")]

# ############################################################################
# General expected behavior

test_that("error with inappropriate method argument", {
  expect_error(umap(i4, method="non_existent_method"))
})

test_that("reproducible output when seed is set", {
  conf <- umap.defaults
  conf$random_state <- 102030405
  conf$init <- "random"
  conf$n_epochs <- 2
  # start rng in this environment
  set.seed(9001)
  r1 <- runif(1)

  # restart rng in this environment
  set.seed(9001)
  result.a <- umap(i4, conf)
  result.b <- umap(i4, conf)
  # even though umap uses random numbers,
  # seed in parent should remain unchanged
  r2 <- runif(1)
  
  abdiff <- sum(abs(result.a$laytout-result.b$layout))
  expect_equal(result.a, result.b, tolerance=1e-4)
  expect_equal(r1, r2, tolerance=1e-4)
})

test_that("output with rownames", {
  conf <- umap.defaults
  conf$n_epochs <- 2
  conf$init <- "random"
  data <- i4
  rownames(data) <- paste0("S", seq_len(nrow(i4)))
  result <- umap(data, conf)
  expect_equal(rownames(result$layout), rownames(data))
})

# ############################################################################
# Settings parameters without configuration object

test_that("accept parameters in main function", {
  conf <- umap.defaults
  conf$n_neighbors <- 5
  conf$n_epochs <- 2
  conf$init <- "random"
  data <- i4
  # override n_neighbors explicitly 
  result <- umap(data, conf, n_neighbors=3)
  expect_equal(result$config$n_neighbors, 3)
  expect_equal(ncol(result$knn$indexes), 3)
})

test_that("supply knn in main", {
  conf <- umap.defaults
  conf$n_neighbors <- 5
  conf$n_epochs <- 2
  conf$init <- "random"
  data <- i4
  result1 <- umap(data, conf)
  # supply knn, result2 should not recompute knn
  result2 <- umap(data, conf, knn=result1$knn)
  expect_equal(result1$knn, result2$knn)
})

# ############################################################################
# Logging 

test_that("log messages in verbose mode", {
  conf <- umap.defaults
  conf$verbose <- TRUE
  conf$init <- "random"
  conf$n_epochs <- 0
  expect_message(umap(i4, conf), "starting")
  expect_message(umap(i4, conf), "creating")
})

test_that("log messages during prediction verbose mode", {
  conf <- umap.defaults
  conf$verbose <- TRUE
  conf$init <- "random"
  conf$n_epochs <- 0
  u4 <- suppressMessages(umap(i4, conf))
  expect_message(predict(u4, i4), "creating")
  expect_message(predict(u4, i4), "optimizing")
})

test_that("use of supplied knn", {
  conf <- umap.defaults
  conf$n_neighbors <- 3
  conf$n_epochs <- 2
  conf$init <- "random"
  data <- i4
  # override n_neighbors explicitly 
  result1 <- umap(data, conf)
  # expect log message
  expect_message(umap(data, conf, verbose=TRUE, knn=result1$knn), "supplied")
})

# ############################################################################
# Unusual datasets

test_that("spectral layout on two component data", {
  ilarge <- rbind(i4, i4+100)
  conf <- umap.defaults
  conf$n_epochs <- 0
  result <- umap(ilarge, conf)$layout
  expect_equal(dim(result), c(nrow(ilarge), 2))
})

test_that("spectral layout aborts and uses random init with small datasets", {
  ismall <- i4[1:3,]
  conf <- umap.defaults
  conf$n_epochs <- 2
  conf$n_neighbors <- 3
  expect_warning(umap(ismall, conf), "init")
})