tests/testthat/test-extractors.R

In FELLA: Interpretation and enrichment for metabolomics data

context("Extractor functions")

# Load data to test
# test.env <- new.env(parent = environment())
test.env <- environment()
data("FELLA.sample", package = "FELLA", envir = test.env)
data("input.sample", package = "FELLA", envir = test.env)

test_that("getCom extractor", {
    categories <- c(as.list(1:5), listCategories())
    
    plyr::l_ply(categories, function(categ) {
        temporary <- try(FELLA:::getCom(
            data = FELLA.sample, 
            level = categ, 
            format = "name"))
        
        expect_is(temporary, "character")
        expect_gt(length(temporary), 0)
        
        temporary <- try(FELLA:::getCom(
            data = FELLA.sample, 
            level = categ, 
            format = "id"))
        
        expect_is(temporary, "integer")
        expect_named(temporary)
        expect_gt(length(temporary), 0)
        
        invisible()
    })
})

test_that("getGraph extractor", {
    expect_is(FELLA:::getGraph(FELLA.sample), "igraph")
    expect_is(FELLA:::getInfo(FELLA.sample), "character")
})

test_that("getMatrix extractor", {
    expect_is(FELLA:::getMatrix(FELLA.sample, "hypergeom"), "lgCMatrix")
    expect_is(FELLA:::getMatrix(FELLA.sample, "diffusion"), "matrix")
    expect_is(FELLA:::getMatrix(FELLA.sample, "pagerank"), "matrix")
})

test_that("getName extractor", {
    temp <- FELLA:::getCom(FELLA.sample, level = 3)
    ans_temp <- FELLA::getName(FELLA.sample, id = temp)
    
    expect_is(ans_temp, "list")
    expect_gt(length(ans_temp), 0)
    expect_is(ans_temp[[1]], "character")
    expect_gt(length(ans_temp[[1]]), 0)
})

test_that("getSums extractor", {
    plyr::l_ply(
        c("diffusion", "pagerank"), 
        function(method) {
            plyr::l_ply(
                c(TRUE, FALSE), 
                function(squared) {
                    sums <- FELLA:::getSums(
                        data = FELLA.sample, 
                        method = "diffusion", 
                        squared = FALSE)
                    
                    expect_named(sums)
                    expect_is(sums, "numeric")
                    expect_gt(length(sums), 0)
                    expect_true(all(sums > 0))
                }
            )
        }
    )
})