tests/testthat/test-PhIPData.R

In athchen/PhIPData: Container for PhIP-Seq Experiments

context("Base PhIPData API functions work as expected.")

# source("setup.R")

# Test missing params ----------------------------------------
test_that("valid PhIPData objects are created when there are missing inputs.", {

    # No assay, no metadata
    expect_is(PhIPData(), "PhIPData")

    # No assay, only metadata
    expect_is(PhIPData(peptideInfo = virscan_info), "PhIPData")
    expect_is(PhIPData(sampleInfo = sampleInfo), "PhIPData")

    # only one assay/input is present, no metadata
    expect_is(PhIPData(counts = counts), "PhIPData")
    expect_is(PhIPData(logfc = logfc), "PhIPData")
    expect_is(PhIPData(prob = prob), "PhIPData")

    # one assay and metadata
    expect_is(PhIPData(counts = counts, sampleInfo = sampleInfo), "PhIPData")
    expect_is(PhIPData(counts = counts, peptideInfo = virscan_info), "PhIPData")
    expect_is(PhIPData(
        counts = counts, peptideInfo = virscan_info,
        sampleInfo = sampleInfo
    ), "PhIPData")

    # only two assays are present, no metadata
    expect_is(PhIPData(counts = counts, logfc = logfc), "PhIPData")
    expect_is(PhIPData(counts = counts, prob = prob), "PhIPData")
    expect_is(PhIPData(logfc = logfc, prob = prob), "PhIPData")

    # only two assays and metadata
    expect_is(PhIPData(
        counts = counts, logfc = logfc,
        sampleInfo = sampleInfo
    ), "PhIPData")
    expect_is(PhIPData(
        counts = counts, logfc = logfc,
        peptideInfo = virscan_info
    ), "PhIPData")
    expect_is(
        PhIPData(
            counts = counts, logfc = logfc,
            peptideInfo = virscan_info, sampleInfo = sampleInfo
        ),
        "PhIPData"
    )

    # all 3 assays, no metadata
    expect_is(PhIPData(counts = counts, logfc = logfc, prob = prob), "PhIPData")

    # all 3 assays and metadata
    expect_is(PhIPData(
        counts = counts, logfc = logfc, prob = prob,
        sampleInfo = sampleInfo
    ), "PhIPData")
    expect_is(PhIPData(
        counts = counts, logfc = logfc, prob = prob,
        peptideInfo = virscan_info
    ), "PhIPData")
    expect_is(
        PhIPData(
            counts = counts, logfc = logfc, prob = prob,
            peptideInfo = virscan_info, sampleInfo = sampleInfo
        ),
        "PhIPData"
    )

    # peptide data is missing positional information
    nopos_pepInfo <- dplyr::select(virscan_info, -contains("pos"))
    expect_is(
        PhIPData(
            counts = counts, logfc = logfc, prob = prob,
            peptideInfo = nopos_pepInfo, sampleInfo = sampleInfo
        ),
        "PhIPData"
    )
})

# Test name-fixing code ----------------------------------------
# Function to quickly compare names
expect_names <- function(object, list) {
    names <- dimnames(object)
    return(all(names[[1]] == list[[1]]) & all(names[[2]] == list[[2]]))
}

test_that("dimension names are set correctly when inputs are mismatched", {
    assay_list <- list(counts = counts, logfc = logfc, prob = prob)

    for (assay in c("counts", "prob")) {
        rownames(assay_list[[assay]]) <-
            paste0(assay, "_", rownames(assay_list[[assay]]))
        colnames(assay_list[[assay]]) <-
            paste0(assay, "_", colnames(assay_list[[assay]]))
    }
    colnames(assay_list[["logfc"]]) <-
        paste0("logfc_", colnames(assay_list[["logfc"]]))

    # Check defaults work
    expect_true(expect_names(
        PhIPData(
            assay_list[["counts"]],
            assay_list[["logfc"]],
            assay_list[["prob"]],
            virscan_info,
            sampleInfo
        ),
        list(
            rownames(peptideInfo),
            rownames(sampleInfo)
        )
    ))

    # Check single default input works as expected
    expect_true(expect_names(
        PhIPData(assay_list[["counts"]],
            assay_list[["logfc"]],
            assay_list[["prob"]],
            virscan_info,
            sampleInfo,
            .defaultNames = "counts"
        ),
        dimnames(assay_list[["counts"]])
    ))

    expect_true(expect_names(
        PhIPData(assay_list[["counts"]],
            assay_list[["logfc"]],
            assay_list[["prob"]],
            virscan_info,
            sampleInfo,
            .defaultNames = "logfc"
        ),
        dimnames(assay_list[["logfc"]])
    ))

    expect_true(expect_names(
        PhIPData(assay_list[["counts"]],
            assay_list[["logfc"]],
            assay_list[["prob"]],
            virscan_info,
            sampleInfo,
            .defaultNames = "prob"
        ),
        dimnames(assay_list[["prob"]])
    ))

    # check double default and extra default input do not generate errors
    expect_true(expect_names(
        PhIPData(assay_list[["counts"]],
            assay_list[["logfc"]],
            assay_list[["prob"]],
            virscan_info,
            sampleInfo,
            .defaultNames = c(
                "counts", "logfc",
                "extraneous"
            )
        ),
        list(
            rownames(assay_list[["counts"]]),
            colnames(assay_list[["logfc"]])
        )
    ))
})

# Test error-causing inputs ----------------------------------------
test_that("invalid inputs return proper errors", {

    # negative counts
    expect_error(
        PhIPData(counts = matrix(-15:14, nrow = 5)),
        "'counts' cannot have negative entries."
    )

    # incompatible dimensions
    expect_error(
        PhIPData(
            counts = counts,
            logfc = DataFrame(matrix(nrow = 5, ncol = 5))
        ),
        "The number of .* differs across inputs"
    )

    # invalid default behavior for mismatched names
    # (only a problem names are mismatched)
    rownames(logfc) <- paste0("logfc_", rownames(logfc))
    expect_error(
        PhIPData(counts, logfc, prob,
            virscan_info, sampleInfo,
            .defaultNames = "test"
        ),
        "Invalid '.defaultNames' supplied."
    )

    colnames(logfc) <- paste0("logfc_", colnames(logfc))
    expect_error(
        PhIPData(counts, logfc, prob,
            virscan_info, sampleInfo,
            .defaultNames = "test"
        ),
        "Invalid '.defaultNames' supplied."
    )
})

# Test getters ----------------------------------------
test_that("getter functions return objects of the expected class", {
    phip_obj <- PhIPData(
        counts = counts, logfc = logfc, prob = prob,
        sampleInfo = sampleInfo, peptideInfo = virscan_info
    )

    expect_is(counts(phip_obj), "matrix")
    expect_is(logfc(phip_obj), "matrix")
    expect_is(prob(phip_obj), "matrix")
    expect_is(peptideInfo(phip_obj), "GRanges")
    expect_is(sampleInfo(phip_obj), "DataFrame")
})

# Test setters ----------------------------------------
# 1. Check that replacement works and
# 2. Replacement fixes mismatched sample/peptide names.
test_that("setter functions change the object as desired", {
    phip_obj <- PhIPData(
        counts = counts, logfc = logfc, prob = prob,
        sampleInfo = sampleInfo, peptideInfo = virscan_info
    )

    # Check assay replacement; newinfo has different names
    replacement_matrix <- matrix(sample(1:1e6, n_samples * n_peptides,
        replace = TRUE
    ), nrow = n_peptides)

    expect_error(
        assays(phip_obj) <- list(
            assay_1 = replacement_matrix,
            assay_2 = replacement_matrix
        ),
        paste0(
            "`counts`, `logfc`, and `prob` assays must be included ",
            "in a PhIPData object. The following assays are ",
            "missing: counts, logfc, prob."
        )
    )
    assays(phip_obj) <- list(
        counts = replacement_matrix,
        logfc = replacement_matrix,
        prob = replacement_matrix
    )
    expect_equal(unname(counts(phip_obj)), replacement_matrix)
    expect_equal(unname(logfc(phip_obj)), replacement_matrix)
    expect_equal(unname(prob(phip_obj)), replacement_matrix)

    assay(phip_obj) <- counts
    expect_equal(counts(phip_obj), counts)
    assay(phip_obj, 2) <- logfc
    expect_equal(logfc(phip_obj), logfc)
    assay(phip_obj, "prob") <- prob
    expect_equal(prob(phip_obj), prob)

    counts(phip_obj) <- logfc(phip_obj) <- prob(phip_obj) <- replacement_matrix
    expect_equal(unname(counts(phip_obj)), replacement_matrix)
    expect_equal(unname(logfc(phip_obj)), replacement_matrix)
    expect_equal(unname(prob(phip_obj)), replacement_matrix)

    # Check that invalid replacement generates warning
    expect_error(
        counts(phip_obj) <- matrix(-1L, nrow = n_peptides, ncol = n_samples),
        "'counts' cannot have negative entries."
    )

    # Check peptideInfo replacement; new info has different rownames
    peptideInfo(phip_obj) <- virscan_info[, 1:10]
    pep_tidied <- .tidyPeptideInfo(
        virscan_info[, 1:10],
        dimnames(phip_obj)[[1]]
    )
    pep_expect <- GenomicRanges::GRanges(
        seqnames = dimnames(phip_obj)[[1]],
        ranges = IRanges::IRanges(
            start = pep_tidied[["pep_start"]],
            end = pep_tidied[["pep_end"]]
        )
    )

    mcols(pep_expect) <- pep_tidied[["pep_meta"]]

    expect_equal(unname(peptideInfo(phip_obj)), pep_expect)

    # Check sampleInfo replacement, new info has different rownames
    sampleInfo$ART <- sample(c("yes", "no"), n_samples, replace = TRUE)
    sampleInfo(phip_obj) <- sampleInfo

    expect_equal(sampleInfo(phip_obj), sampleInfo)
})

test_that("assays can be added and removed", {
    phip_obj <- PhIPData(
        counts = counts, logfc = logfc, prob = prob,
        sampleInfo = sampleInfo, peptideInfo = virscan_info
    )

    replacement_matrix <- matrix(runif(n_samples * n_peptides, min = 1, max = 1e6),
        nrow = n_peptides
    )

    expect_error(
        assay(phip_obj, "counts") <- NULL,
        paste0(
            "`counts`, `logfc`, and `prob` assays must be included ",
            "in a PhIPData object. The following assays are ",
            "missing: counts"
        )
    )
    assay(phip_obj, "new_assay") <- replacement_matrix
    expect_equal(
        unname(assay(phip_obj, "new_assay")),
        replacement_matrix
    )
    assay(phip_obj, "new_assay") <- NULL
    expect_true(!"new_assay" %in% assayNames(phip_obj))
})

# Test coercion functions -----------
test_that("coercion functions work as expected", {
    phip_obj <- PhIPData(
        counts = counts, logfc = logfc, prob = prob,
        sampleInfo = sampleInfo, peptideInfo = virscan_info
    )

    expect_is(as(phip_obj, "list"), "list")
    expect_is(as(phip_obj, "List"), "List")
    expect_is(as(phip_obj, "DGEList"), "DGEList")
    expect_is(as(phip_obj, "DataFrame"), "DataFrame")

    expect_is(as(as(phip_obj, "list"), "PhIPData"), "PhIPData")
    expect_is(as(as(phip_obj, "List"), "PhIPData"), "PhIPData")
    expect_is(as(as(phip_obj, "DGEList"), "PhIPData"), "PhIPData")
})