tests/testthat/test-DelayedArray.R

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

test_that("DelayedArray works", {
    
    if (!is_32bit()) {
        #### Setup data ####
        cortex_mrna <- ewceData::cortex_mrna()
        expMatrix <- DelayedArray::DelayedArray(cortex_mrna$exp)
        # ctd <- ewceData::ctd()
        ctd <- list(
            level1 = list(),
            level2 = list()
        )
        ctd[[1]][["annot"]] <- cortex_mrna$annot$level1class
        #### Set DelayedArray parameters ####
        EWCE:::assign_cores(worker_cores = 1)
        DelayedArray:::set_verbose_block_processing(verbose = TRUE)

        #### Test calculate_meanexp_for_level ####
        ctd_oneLevel <- EWCE:::calculate_meanexp_for_level(
            ctd_oneLevel = ctd[[1]],
            expMatrix = expMatrix
        )
        testthat::expect_length(ctd_oneLevel, 2)
        testthat::expect_true(all(c("annot", "mean_exp") %in% names(ctd_oneLevel)))

        #### Test calculate_specificity_for_level ####
        ctd_oneLevel_mod <- EWCE:::calculate_specificity_for_level(
            ctd_oneLevel = ctd_oneLevel
        )
        testthat::expect_length(ctd_oneLevel_mod, 3)
        testthat::expect_true(
            all(c("annot", "mean_exp", "specificity") %in% names(ctd_oneLevel_mod))
        )

        #### Test delayedarray_normalize ####
        exp_norm <- EWCE:::delayedarray_normalize(
            exp = expMatrix,
            log_norm = TRUE,
            min_max = TRUE
        ) 
        testthat::expect_equal(dim(exp_norm), dim(expMatrix))
        
        #### Test DelayedArray as input to sct_normalize ####
        exp_norm_sct <- EWCE::sct_normalize(expMatrix)
        testthat::expect_true(EWCE:::is_sparse_matrix(exp_norm_sct))
    }
})