tests/testthat/test-d-dataconversion.R

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

library(omnideconv)

sc_object_small <- system.file("small_test_data", "sc_object_small.csv",
  package = "omnideconv", mustWork = TRUE
) %>%
  utils::read.csv(., row.names = 1) %>%
  as.matrix(.)

cell_annotations_small <- system.file("small_test_data", "cell_annotations_small.txt",
  package = "omnideconv", mustWork = TRUE
) %>%
  readr::read_lines(.)

test_that("Matrix/SingleCellExperiment conversion works", {
  sce <- matrix_to_singlecellexperiment(sc_object_small, cell_annotations_small)
  expect_identical(
    info = "Conversion from Matrix to SingleCellExperiment had no error",
    object = typeof(sce), expected = "S4"
  )
  X <- as.list(SummarizedExperiment::assays(sce))[[1]]
  labels <- SingleCellExperiment::colData(sce)$label
  expect_equal(info = "SCE Matrix is correct", object = X, expected = sc_object_small)
  expect_equal(
    info = "SCE annotation vector is correct", object = labels,
    expected = cell_annotations_small
  )

  matrix_and_annotation <- singlecellexperiment_to_matrix(sce, cell_type_column_name = "label")
  expect_identical(
    info = "Conversion from SingleCellExperiment to Matrix had no error",
    object = typeof(matrix_and_annotation), expected = "list"
  )
  matrix <- matrix_and_annotation$matrix
  annotation <- matrix_and_annotation$annotation_vector
  expect_equal(info = "Matrix is correct", object = matrix, expected = sc_object_small)
  expect_equal(
    info = "Annotation vector is correct", object = annotation,
    expected = cell_annotations_small
  )
})



test_that("SingleCellExperiment/Anndata conversion works", {
  ad <- anndata::AnnData(
    X = matrix(1:6, nrow = 2),
    obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
    var = data.frame(type = c(1L, 2L, 3L), row.names = c("var1", "var2", "var3")),
    layers = list(
      spliced = matrix(4:9, nrow = 2),
      unspliced = matrix(8:13, nrow = 2)
    ),
    obsm = list(
      ones = matrix(rep(1L, 10), nrow = 2),
      rand = matrix(rnorm(6), nrow = 2),
      zeros = matrix(rep(0L, 10), nrow = 2)
    ),
    varm = list(
      ones = matrix(rep(1L, 12), nrow = 3),
      rand = matrix(rnorm(6), nrow = 3),
      zeros = matrix(rep(0L, 12), nrow = 3)
    ),
    uns = list(
      a = 1,
      b = data.frame(i = 1:3, j = 4:6, value = runif(3)),
      c = list(c.a = 3, c.b = 4)
    )
  )

  sce_converted <- anndata_to_singlecellexperiment(ad)


  expect_equal(
    info = "Anndata conversion to SCE did not produce an error",
    object = typeof(sce_converted), expected = "S4"
  )
  expect_equal(
    info = "SCE conversion to Anndata did not produce an error",
    object = typeof(ad), expected = "environment"
  )
})

test_that("SingleCellExperiment/Anndata conversion does not lose information", {
  # Fails if we use type = c(1L, 2L, 3L) because R internally transforms dataframes
  # of integers to dataframes of numerics and then the classes dont match
  ad <- anndata::AnnData(
    X = matrix(1:6, nrow = 2),
    obs = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
    var = data.frame(type = c(1, 2, 3), row.names = c("var1", "var2", "var3")),
    layers = list(
      spliced = matrix(4:9, nrow = 2),
      unspliced = matrix(8:13, nrow = 2)
    )
  )

  sce <- SingleCellExperiment::SingleCellExperiment(
    list(
      X = t(matrix(1:6, nrow = 2)), spliced = t(matrix(4:9, nrow = 2)),
      unspliced = t(matrix(8:13, nrow = 2))
    ),
    colData = data.frame(group = c("a", "b"), row.names = c("s1", "s2")),
    rowData = data.frame(type = c(1, 2, 3), row.names = c("var1", "var2", "var3"))
  )

  sce_converted <- omnideconv:::anndata_to_singlecellexperiment(ad)

  ad_converted <- omnideconv:::singlecellexperiment_to_anndata(sce)


  expect_equal(
    info = "Anndata conversion to SCE did not produce an error",
    object = typeof(sce_converted), expected = "S4"
  )
  expect_equal(
    info = "SCE conversion to Anndata did not produce an error",
    object = typeof(ad), expected = "environment"
  )
  expect_equal(
    info = "Conversion from Anndata to SCE is correct",
    object = sces_are_identical(sce, sce_converted), expected = TRUE
  )
  expect_equal(
    info = "Conversion from SCE to Anndata is correct",
    object = anndata_is_identical(ad, ad_converted), expected = TRUE
  )
})