tests/testthat/test_rbindFill.R

In MsCoreUtils: Core Utils for Mass Spectrometry Data

test_that("rbindFill works", {
    require("S4Vectors")
    expect_error(rbindFill(1:2, 1:4), "just works for")

    ## matrix
    a <- matrix(1:9, nrow = 3, ncol = 3)
    colnames(a) <- c("a", "b", "c")
    b <- matrix(1:12, nrow = 3, ncol = 4)
    colnames(b) <- c("b", "a", "d", "e")
    res <- rbindFill(a, b)
    expect_equal(colnames(res), c("a", "b", "c", "d", "e"))
    expect_equal(class(res), class(a))
    expect_equal(res[, "a"], c(a[, "a"], b[, "a"]))
    expect_equal(res[, "b"], c(a[, "b"], b[, "b"]))
    expect_equal(res[, "d"], c(NA, NA, NA, b[, "d"]))

    res2 <- rbindFill(list(a, b))
    expect_identical(res, res2)

    res <- rbindFill(a, b[, c("b", "a")])
    expect_equal(colnames(res), c("a", "b", "c"))
    expect_equal(res[, "a"], c(a[, "a"], b[, "a"]))

    ## DataFrame
    a <- DataFrame(a = 1:4, b = FALSE, c = letters[1:4])
    b <- DataFrame(d = 1:4, b = TRUE)
    res <- rbindFill(a, b)
    expect_equal(colnames(res), c("a", "b", "c", "d"))
    expect_equal(res$a, c(1:4, NA, NA, NA, NA))
    expect_equal(res$b, rep(c(FALSE, TRUE), each = 4))

    b$e <- Rle(1, 4)
    res <- rbindFill(a, b)
    expect_identical(res$e, Rle(c(NA_integer_, 1), c(4, 4)))

    a$e <- Rle(2, 4)
    res <- rbindFill(a, b)
    expect_identical(res$e, Rle(c(2, 1), c(4, 4)))

    res <- rbindFill(a, b, DataFrame(z = factor(1:5)))
    expect_identical(res$z, factor(c(rep(NA, nrow(a) + nrow(b)), 1:5)))
    expect_identical(res$a, c(1:4, rep(NA, nrow(b) + 5)))
    expect_identical(res$b, c(rep(FALSE, nrow(a)), rep(TRUE, nrow(b)), rep(NA, 5)))

    ## DataFrame containing SimpleList.
    a$mz <- list(1:3, 1:4, 1:2, 1:3)
    res <- rbindFill(a, b)
    expect_true(is(res$mz, "list"))
    expect_true(all(unlist(is.na(res$mz[5:8]))))
    expect_true(is.na(res$mz[[5]]))

    ## If the first DataFrame doesn't contain a SimpleList but the second one
    res <- DataFrame(d = c(1L:4L, rep(NA_real_, 4L)),
                     b = rep(c(TRUE, FALSE), each = 4L),
                     e = Rle(1:2, 4),
                     a = c(rep(NA_real_, 4L), 1L:4L),
                     c = c(rep(NA_character_, 4L), letters[1L:4L]))
    res$mz <- list(NA, NA, NA, NA,
                   1:3, 1:4, 1:2, 1:3)
    expect_equal(rbindFill(b, a), res)

    ## Ensure data types are correct after merging.
    a <- DataFrame(int = c(1L, 1L), int_rle = Rle(c(1L, 1L)),
                   log = c(TRUE, FALSE), log_rle = Rle(c(FALSE, FALSE)))
    b <- DataFrame(real = c(1.2, 1.5), real_rle = Rle(c(1.2, 1.5)))
    res <- rbindFill(a, b)
    expect_true(is.integer(res$int))
    expect_true(is.integer(res$int_rle@values))
    expect_true(is.logical(res$log))
    expect_true(is.logical(res$log_rle@values))
    expect_true(is.double(res$real))
    expect_true(is.double(res$real_rle@values))

    ## works with a single DataFrame or data.frame
    expect_equal(rbindFill(a), a)
    b <- data.frame(a = 1:3)
    expect_equal(rbindFill(b), b)
})