tests/testthat/test_scale.R

In jlmelville/uwot: The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction

library(uwot)
context("Scaling")

iris10_sd <- apply(iris10, 2, sd)
iris10_mean <- apply(iris10, 2, mean)

iris10_none <- scale_input(iris10, scale_type = FALSE)
expect_equal(apply(iris10_none, 2, sd), iris10_sd)
expect_equal(apply(iris10_none, 2, mean), iris10_mean)

iris10_scale <- scale_input(iris10, scale_type = TRUE)
expect_equal(apply(iris10_scale, 2, sd), rep(1, 4), check.attributes = FALSE)
expect_equal(apply(iris10_scale, 2, mean), rep(0, 4), check.attributes = FALSE)

# "scale" and "z" and TRUE are synonyms
expect_equal(scale_input(iris10, scale_type = "scale"), iris10_scale)
expect_equal(scale_input(iris10, scale_type = "Z"), iris10_scale)

iris10_maxabs <- scale_input(iris10, scale_type = "maxabs")
expect_equal(apply(iris10_maxabs, 2, mean), rep(0, 4), check.attributes = FALSE)
expect_equal(max(abs(iris10_maxabs)), 1)

iris10_range <- scale_input(iris10, scale_type = "range")
expect_equal(max(iris10_range), 1)
expect_equal(min(iris10_range), 0)

iris10_colrange <- scale_input(iris10, scale_type = "colrange")
expect_equal(apply(iris10_colrange, 2, max), rep(1, 4), check.attributes = FALSE)
expect_equal(apply(iris10_colrange, 2, min), rep(0, 4), check.attributes = FALSE)

test_that("scaling applied outside umap should not appear in the model", {
  iris10s <- scale(iris10)
  iris10s_umap0 <-
    umap(
      iris10s,
      n_neighbors = 4,
      n_epochs = 0,
      init = "rand",
      ret_model = TRUE,
      scale = FALSE
    )
  expect_null(iris10s_umap0$scale_info)

  iris10s_umap0s <-
    umap(
      iris10s,
      n_neighbors = 4,
      n_epochs = 0,
      init = "rand",
      ret_model = TRUE,
      scale = TRUE
    )
  expect_equal(
    names(iris10s_umap0s$scale_info),
    c("scaled:center", "scaled:scale", "scaled:nzvcols")
  )
})