tests/testthat/test-exploreModelMatrix.R

In ExploreModelMatrix: Graphical Exploration of Design Matrices

test_that("ExploreModelMatrix fails with incorrect inputs", {
  sampleData <- data.frame(
    genotype = rep(c("A", "B"), each = 4),
    treatment = rep(c("trt", "ctrl"), 4),
    stringsAsFactors = FALSE
  )
  designFormula <- ~genotype

  expect_error(ExploreModelMatrix(sampleData = 1,
                                  designFormula = designFormula))
  expect_error(ExploreModelMatrix(sampleData = as.matrix(sampleData),
                                  designFormula = designFormula))
  expect_error(ExploreModelMatrix(sampleData = as.list(sampleData),
                                  designFormula = designFormula))
  expect_error(ExploreModelMatrix(sampleData = sampleData,
                                  designFormula = "~genotype"))
  sampleData[1, 1] <- NA
  expect_error(ExploreModelMatrix(sampleData = sampleData,
                                  designFormula = designFormula),
               regex = "can not contain NA values")
})

test_that("ExploreModelMatrix generates a shiny app object", {
  sampleData <- data.frame(
    genotype = rep(c("A", "B"), each = 4),
    treatment = rep(c("trt", "ctrl"), 4),
    stringsAsFactors = FALSE
  )

  expect_s3_class(ExploreModelMatrix(sampleData = sampleData,
                                     designFormula = ~genotype),
                  "shiny.appobj")
  expect_s3_class(ExploreModelMatrix(sampleData = sampleData,
                                     designFormula = ~0 + genotype),
                  "shiny.appobj")

  ## DataFrame input
  sampleData <- S4Vectors::DataFrame(
    genotype = rep(c("A", "B"), each = 4),
    treatment = rep(c("trt", "ctrl"), 4)
  )

  expect_s3_class(ExploreModelMatrix(sampleData = sampleData,
                                     designFormula = ~genotype),
                  "shiny.appobj")
  expect_s3_class(ExploreModelMatrix(sampleData = sampleData,
                                     designFormula = ~0 + genotype),
                  "shiny.appobj")
})

test_that(".IsValidFormula works as expected", {
  sampleData <- data.frame(
    genotype = rep(c("A", "B"), each = 4),
    treatment = rep(c("trt", "ctrl"), 4),
    stringsAsFactors = FALSE
  )

  expect_true(ExploreModelMatrix:::.IsValidFormula(
    ~genotype, sampleData
  ))
  expect_true(ExploreModelMatrix:::.IsValidFormula(
    ~0 + genotype, sampleData
  ))
  expect_false(ExploreModelMatrix:::.IsValidFormula(
    ~genotyp, sampleData
  ))
  expect_false(ExploreModelMatrix:::.IsValidFormula(
    "~genotype", sampleData
  ))
})

test_that(".CheckNumericArguments works as expected", {
  expect_true(ExploreModelMatrix:::.CheckNumericArguments(1))
  expect_true(ExploreModelMatrix:::.CheckNumericArguments(1, 2))
  expect_true(ExploreModelMatrix:::.CheckNumericArguments(1, pi))
  expect_true(ExploreModelMatrix:::.CheckNumericArguments("1"))
  expect_false(ExploreModelMatrix:::.CheckNumericArguments("str"))
  expect_false(ExploreModelMatrix:::.CheckNumericArguments(0, "str"))
  expect_true(ExploreModelMatrix:::.CheckNumericArguments(1, TRUE))
})