tests/testthat/test-string_db.R

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

test_that("stringDBhomoSapiens: Will parse a valid (fake) dataset", {
    testthat::local_mocked_bindings(
        download.file = function(url, destfile, method, ...) {
            # write a file with some data
            readr::write_delim(prepareMockInteractions(), destfile, delim = " ")
        },
        .package = "utils"
    )

    interactions <- stringDBhomoSapiens(scoreThreshold = 150)

    interactions |>
        expect_s3_class(c("tbl", "tbl_df", "data.frame"))

    interactions$combined_score |>
        expect_length(4) |>
        vapply(expect_gte, numeric(1L), 150)
})

test_that("buildStringNetwork: Can build network", {
    testthat::local_mocked_bindings(
        download.file = function(url, destfile, method, ...) {
            # write a file with some data
            readr::write_delim(prepareMockInteractions(), destfile, delim = " ")
        },
        .package = "utils"
    )

    interactions <- stringDBhomoSapiens(scoreThreshold = 150)

    # test deprecated parameters
    buildStringNetwork(string.tbl = interactions) |>
        lifecycle::expect_deprecated("stringTbl")
    buildStringNetwork(interactions, use.names = "protein") |>
        lifecycle::expect_deprecated("useNames")

    network <- buildStringNetwork(interactions)

    network |>
        expect_s4_class(c("dgCMatrix")) |>
        expect_length(64)

    (as.vector(network) != 0) |>
        sum() |>
        expect_equal(4)
})

test_that("buildStringNetwork: Can build network with external and ensembl", {
    testthat::local_mocked_bindings(
        protein2EnsemblGeneNames = function(ensemblProteins, ...) {
            data.frame(
                ensembl_peptide_id = ensemblProteins,
                ensembl_gene_id    = paste0("ens_", ensemblProteins),
                external_gene_name = paste0("gene_", ensemblProteins),
                stringsAsFactors   = FALSE
            )
        },
        geneNames = function(ensemblGenes, ...) {
            data.frame(
                ensembl_gene_id = ensemblGenes,
                external_gene_name = paste0("gene_", ensemblGenes),
                stringsAsFactors = FALSE
            )
        }
    )

    interactions <- stringDBhomoSapiens(scoreThreshold = 150)
    (network1 <- buildStringNetwork(interactions, useNames = "external")) |>
        colnames() |>
        expect_match("gene_")

    (network2 <- buildStringNetwork(interactions, useNames = "ensembl")) |>
        colnames() |>
        expect_match("ens_")

    network1 |>
        expect_s4_class(c("dgCMatrix")) |>
        expect_length(64)

    network2 |>
        expect_s4_class(c("dgCMatrix")) |>
        expect_length(64)

    (as.vector(network1) != 0) |>
        sum() |>
        expect_equal(4)

    (as.vector(network2) != 0) |>
        sum() |>
        expect_equal(4)
})

test_that("calculateCombinedScore: removeText will return different score", {
    testthat::local_mocked_bindings(
        download.file = function(url, destfile, method, ...) {
            # write a file with some data
            readr::write_delim(prepareMockInteractions(), destfile, delim = " ")
        },
        .package = "utils"
    )

    score1 <- stringDBhomoSapiens(scoreThreshold = 150, removeText = TRUE) |>
        magrittr::extract2("combined_score")
    score2 <- stringDBhomoSapiens(scoreThreshold = 150, removeText = FALSE) |>
        magrittr::extract2("combined_score")

    expect_failure(
        expect_equal(score1, score2, tolerance = 1e-6)
    )
})