tests/testthat/test-mx_dataset.R

In mxnorm: Apply Normalization Methods to Multiplexed Images

test_that("trim works", {
    x = trim_dataset(mx_sample,"slide_id","image_id",c("marker1_vals"),c("metadata1_vals"))
    y = trim_dataset(mx_sample,"slide_id","image_id",c("marker1_vals"),NULL)

    ## trims correctly
    expect_equal(any(c("marker2_vals","marker_3_vals") %in% colnames(x)),FALSE)

    ## trims correctly with metadata
    expect_equal(any(c("marker2_vals","marker_3_vals","metadata1_vals") %in% colnames(y)),FALSE)
})

test_that("trim error messages work", {
    ## catches columns that DNE
    expect_error(trim_dataset(mx_sample,"slide_id","image_id",c("marker5_vals"),c("metadata1_vals")))

    ## catches columns that DNE without metadata
    expect_error(trim_dataset(mx_sample,"slide_id","image_id",c("marker5_vals"),NULL))
})

test_that("object works", {
    x = mx_dataset(mx_sample, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals"))

    ## s3 object creation works
    expect_equal(class(x),"mx_dataset")

    ## attributes work
    expect_equal(attributes(x)$names, c("data","slide_id","image_id","marker_cols","metadata_cols"))
})

test_that("object error messages works", {
    ## catches incorrect slide_id
    expect_error(new_mx_dataset(mx_sample, 1, "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))

    ## catches incorrect image_id
    expect_error(new_mx_dataset(mx_sample, "slide_id", 1, c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))

    ## catches incorrect structure of mx_sample
    expect_error(new_mx_dataset(matrix(mx_sample), "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
})

test_that("validate works", {
    x <- mx_sample
    y <- mx_sample
    z <- mx_sample

    x$marker1_vals[5] = Inf
    y$marker1_vals[6] = "7"
    z$marker1_vals[7] = NA

    ## catches Inf
    expect_error(mx_dataset(x, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))

    ## catches character
    expect_error(mx_dataset(y, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))

    ## catches NAs
    expect_error(mx_dataset(z, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
})

test_that("metadata catch works",{
    x = mx_dataset(mx_sample,"slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals"))
    x$data = x$data[,-6]
    expect_error(validate_mx_dataset(x))
})