tests/testthat/test-AllClasses.R

In seriph78/COTAN: COexpression Tables ANalysis

library(Matrix)

setLoggingLevel(4L)

options(COTAN.TorchWarning = NULL)

test_that("Empty matrices", {
  expect_identical(dim(emptySparseMatrix()), c(0L, 0L))
  expect_s4_class(emptySparseMatrix(), "dgCMatrix")

  expect_identical(dim(emptySymmetricMatrix()), c(0L, 0L))
  expect_s4_class(emptySymmetricMatrix(), "dspMatrix")
})

test_that("'COTAN' constructor", {
  utils::data("test.dataset", package = "COTAN")

  obj <- COTAN(raw = test.dataset)

  expect_s4_class(obj, "COTAN")

  expect_identical(obj@raw, as(as.matrix(test.dataset), "sparseMatrix"))
})

test_that("'scCOTAN' converters", {
  raw <- matrix(c(1L,  0L, 4L, 2L, 11L, 0L, 6L, 7L, 0L, 9L,
                  10L, 8L, 0L, 0L, 0L,  3L, 0L, 0L, 2L, 0L),
                nrow = 10L, ncol = 20L)
  rownames(raw) <- LETTERS[1L:10L]
  colnames(raw) <- letters[1L:20L]

  tags <- c("GEO:", "scRNAseq method:",
            "starting n. of cells:", "Condition sample:")

  obj <- COTAN(raw = raw)
  obj <- initializeMetaDataset(obj, GEO = "V", sequencingMethod = "10X",
                               sampleCondition = "Test")
  obj <- clean(obj)
  obj <- estimateDispersionBisection(obj)
  obj <- calculateCoex(obj, actOnCells = FALSE, optimizeForSpeed = FALSE)

  coexDF <- set_names(
    as.data.frame(atan(getNormalizedData(obj)[, 1L:2L] - 0.5) / pi * 2.0),
    c(1L, 2L))

  obj <- addClusterization(obj, clName = "clusters",
                           clusters = set_names(rep(colnames(coexDF), 10L),
                                                colnames(raw)),
                           coexDF = coexDF)

  # coerce 'COTAN' -> 'scCOTAN'
  obj_sc <- as(obj, "scCOTAN")

  expect_identical(obj_sc@raw,      obj@raw)
  expect_identical(obj_sc@raw.norm, getNormalizedData(obj))
  expect_identical(obj_sc@coex,     obj@genesCoex)
  expect_identical(obj_sc@nu,       getNu(obj))
  expect_identical(obj_sc@lambda,   getLambda(obj))
  expect_identical(obj_sc@nu,       getNu(obj))
  expect_identical(obj_sc@a,        getDispersion(obj))
  expect_identical(obj_sc@hk,       getFullyExpressedGenes(obj))
  expect_identical(obj_sc@meta,     obj@metaDataset)
  expect_null(obj_sc@yes_yes)
  expect_length(obj_sc@clusters, ncol(obj_sc@raw))
  if (!all(is.na(obj_sc@clusters))) {
    expect_identical(obj_sc@clusters, factorToVector(getClusters(obj)))
    expect_identical(obj_sc@cluster_data, getClusterizationData(obj)[["coex"]])
  } else {
    expect_length(obj_sc@cluster_data, 0L)
  }

  # coerce 'scCOTAN' -> 'COTAN'
  obj2 <- as(obj_sc, "COTAN")

  if (all(flagNotFullyExpressedGenes(obj))) {
    #drop the fe column as it won't appear in the obj2 in this case!
    obj@metaGenes[["feGenes"]] <- NULL
  }
  if (all(flagNotFullyExpressingCells(obj))) {
    #drop the fe column as it won't appear in the obj2 anyway!
    obj@metaCells[["feCells"]] <- NULL
  }

  expect_identical(obj2, obj)
})

gc()