tests/testthat/test-getAnansi.R

In thomazbastiaanssen/anansi: Annotation-Based Analysis of Specific Interactions

test_that("getAnansi", {
    # Combine experiments into MultiAssayExperiment object
    web <- randomWeb(n_samples = 15, n_reps = 1)
    metadata(web)$cat_XYZ <- rep(c("X", "Y", "Z"), 5)
    mae <- as(web, "MultiAssayExperiment")

    expect_error(
        getAnansi(mae, tableY = "wrong_name"),
        "'tableY' must be numeric or character value specifying experiment in experiment(x)",
        fixed = TRUE
    )
    expect_error(
        getAnansi(
            mae,
            tableY = "y",
            tableX = "x",
            return.format = "wrong_input"
        ),
        class = "error"
    )
    expect_error(
        getAnansi(
            mae,
            tableY = "y",
            tableX = "x",
            formula = ~group_ab,
            web = 0
        ),
        "The arguments 'web' should not be used, as they are extracted from 'x'",
        fixed = TRUE
    )
    ### Check identity with original anansi output ###

    table1 <- anansi(
        web = web,
        formula = ~cat_XYZ,
        verbose = FALSE
    )
    list1 <- anansi(
        web = web,
        formula = ~cat_XYZ,
        verbose = FALSE,
        return.format = "list"
    )
    raw1 <- anansi(
        web = web,
        formula = ~cat_XYZ,
        verbose = FALSE,
        return.format = "raw"
    )

    table2 <- getAnansi(
        mae,
        tableY = "y",
        tableX = "x",
        formula = ~cat_XYZ,
        verbose = FALSE
    )
    list2 <- getAnansi(
        mae,
        tableY = "y",
        tableX = "x",
        formula = ~cat_XYZ,
        return.format = "list",
        verbose = FALSE
    )
    raw2 <- getAnansi(
        mae,
        tableY = "y",
        tableX = "x",
        formula = ~cat_XYZ,
        return.format = "raw",
        verbose = FALSE
    )

    expect_identical(table1, table2)
    expect_identical(list1, list2)
    expect_identical(raw1, raw2)
})