tests/testthat/test-Expressed.R

In myTAI: Evolutionary Transcriptomics

context("Test: Expressed() ")

data(PhyloExpressionSetExample)

# adapted from: https://github.com/hadley/dplyr/blob/master/tests/testthat/test-arrange.r
equal_df <- function(df1, df2) {
        rownames(df1) <- NULL
        rownames(df2) <- NULL
        isTRUE(all.equal(df1, df2))
}

nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

test_that("is.ExpressionSet() throughs error when no ExpressionSet is entered to Expressed()",
          {
                  expect_error(
                          Expressed(ExpressionSet = nonStandardExpressionSet,
                                    cut.off       = 1000)
                          )
          })


test_that("error occurs when wrong filter method is specified in Expressed()",
          {
                  expect_error(
                          Expressed(TestExpressionSet_completePES, 1000, "m-set")
                  )
                  
          })

# a test set for a complete PhyloExpressionSet in ExpressionSet notation (standard)
TestExpressionSet_completePES <- PhyloExpressionSetExample[1:10, ]

test_that(
        "correct rows are removed (filtered) from the count table. Method: 'const' and comparison : 'below'",
        {
                expect_true(equal_df(
                        Expressed(TestExpressionSet_completePES, 1000, "const"),
                        TestExpressionSet_completePES[-c(1, 3, 4, 6, 8, 9), ]
                ))
                
        }
)


test_that(
        "correct rows are removed (filtered) from the count table. Method: 'const' and comparison : 'above'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                1000,
                                "const",
                                comparison = "above"
                        ),
                        TestExpressionSet_completePES[c(6, 8, 9), ]
                ))
                
        }
)


test_that(
        "correct rows are removed (filtered) from the count table. Method: 'const' and comparison : 'both'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                c(800, 2000),
                                "const",
                                comparison = "both"
                        ),
                        TestExpressionSet_completePES[c(2, 3, 4, 7), ]
                ))
                
        }
)


test_that("error occurs when no genes fulfill the threshold criteria: comparison = 'below'",
          {
                  expect_error(
                          Expressed(
                                  TestExpressionSet_completePES,
                                  500,
                                  "const",
                                  comparison = "below"
                          ),
                          "None of the genes fulfilles the threshold criteria. Please choose a less conservative threshold or filter method."
                  )
                  
          })

test_that("error occurs when no genes fulfill the threshold criteria: comparison = 'above'",
          {
                  expect_error(
                          Expressed(
                                  TestExpressionSet_completePES,
                                  80000,
                                  "const",
                                  comparison = "above"
                          ),
                          "None of the genes fulfilles the threshold criteria. Please choose a less conservative threshold or filter method."
                  )
                  
          })

test_that("error occurs when no genes fulfill the threshold criteria: comparison = 'both'",
          {
                  expect_error(
                          Expressed(
                                  TestExpressionSet_completePES,
                                  c(1000, 1100),
                                  "const",
                                  comparison = "both"
                          ),
                          "None of the genes fulfilles the threshold criteria. Please choose a less conservative threshold or filter method."
                  )
                  
          })


test_that(
        "correct rows are removed (filtered) from the count table. Method: 'min-set'; comparison = 'below'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                1000,
                                "min-set",
                                comparison = "below"
                        ),
                        TestExpressionSet_completePES[-c(3, 6, 8, 9), ]
                ))
                
        }
)

test_that(
        "correct rows are removed (filtered) from the count table. Method: 'min-set'; comparison = 'above'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                1000,
                                "min-set",
                                comparison = "above"
                        ),
                        TestExpressionSet_completePES[c(3, 6, 8, 9), ]
                ))
                
        }
)


test_that(
        "correct rows are removed (filtered) from the count table. Method: 'min-set'; comparison = 'both'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                c(800, 2000),
                                "min-set",
                                comparison = "both"
                        ),
                        TestExpressionSet_completePES[c(1:4, 6, 7), ]
                ))
                
        }
)


test_that(
        "correct rows are removed (filtered) from the count table. Method: 'n-set'; comparison = 'below'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                800,
                                "n-set",
                                comparison = "below",
                                n = 5
                        ),
                        TestExpressionSet_completePES[-c(6, 8, 9), ]
                ))
                
        }
)


test_that(
        "correct rows are removed (filtered) from the count table. Method: 'n-set'; comparison = 'above'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                2000,
                                "n-set",
                                comparison = "above",
                                n = 3
                        ),
                        TestExpressionSet_completePES[c(1:4, 6:9), ]
                ))
                
        }
)


test_that(
        "correct rows are removed (filtered) from the count table. Method: 'n-set'; comparison = 'both'",
        {
                expect_true(equal_df(
                        Expressed(
                                TestExpressionSet_completePES,
                                c(900, 2000),
                                "n-set",
                                comparison = "both",
                                n = 4
                        ),
                        TestExpressionSet_completePES[c(1, 2, 4, 7), ]
                ))
                
        }
)

test_that(
        "error occurs when n is larger than the number of available stages when choosing method = 'n-set'",
        {
                expect_error(
                        Expressed(TestExpressionSet_completePES, 800, "n-set", n = 8),
                        "n is larger than the number of available stages in your ExpressionSet..."
                )
        }
)


test_that("error occurs when method = 'n-set', but n = NULL", {
        expect_error(
                Expressed(TestExpressionSet_completePES, 800, "n-set"),
                "Please specify the number of stages n for which expresssion levels need to be above the cutoff to be retained in the count table."
        )
})


test_that("n-set with n = 4 computes the same values as min-set for 7 stages; comparison = 'below'",
          {
                  expect_true(equal_df(
                          Expressed(
                                  PhyloExpressionSetExample,
                                  8000,
                                  "n-set",
                                  comparison = "below",
                                  n = 4
                          ),
                          Expressed(
                                  PhyloExpressionSetExample,
                                  8000,
                                  "min-set",
                                  comparison = "below"
                          )
                  ))
                  
          })

test_that("n-set with n = 4 computes the same values as min-set for 7 stages; comparison = 'above'",
          {
                  expect_true(equal_df(
                          Expressed(
                                  PhyloExpressionSetExample,
                                  2000,
                                  "n-set",
                                  comparison = "above",
                                  n = 4
                          ),
                          Expressed(
                                  PhyloExpressionSetExample,
                                  2000,
                                  "min-set",
                                  comparison = "above"
                          )
                  ))
                  
          })

test_that("n-set with n = 4 computes the same values as min-set for 7 stages; comparison = 'both'",
          {
                  expect_true(equal_df(
                          Expressed(
                                  PhyloExpressionSetExample,
                                  c(900, 2000),
                                  "n-set",
                                  comparison = "both",
                                  n = 4
                          ),
                          Expressed(
                                  PhyloExpressionSetExample,
                                  c(900, 2000),
                                  "min-set",
                                  comparison = "both"
                          )
                  ))
                  
          })

test_that("n-set with n = 6 computes the same values as const; comparison = 'below'",
          {
                  expect_true(equal_df(
                          Expressed(
                                  PhyloExpressionSetExample,
                                  2000,
                                  "n-set",
                                  comparison = "below",
                                  n = 6
                          ),
                          Expressed(PhyloExpressionSetExample, 2000, "const", comparison = "below")
                  ))
                  
          })

test_that("n-set with n = 6 computes the same values as const; comparison = 'above'",
          {
                  expect_true(equal_df(
                          Expressed(
                                  PhyloExpressionSetExample,
                                  8000,
                                  "n-set",
                                  comparison = "above",
                                  n = 6
                          ),
                          Expressed(PhyloExpressionSetExample, 8000, "const", comparison = "above")
                  ))
                  
          })

test_that("n-set with n = 6 computes the same values as const; comparison = 'both'",
          {
                  expect_true(equal_df(
                          Expressed(
                                  PhyloExpressionSetExample,
                                  c(900, 2000),
                                  "n-set",
                                  comparison = "both",
                                  n = 6
                          ),
                          Expressed(
                                  PhyloExpressionSetExample,
                                  c(900, 2000),
                                  "const",
                                  comparison = "both"
                          )
                  ))
                  
          })


test_that("error occurs when only one cut.off is specified when selecting comparison = 'both'",
          {
                  expect_error(
                          Expressed(
                                  PhyloExpressionSetExample,
                                  2000,
                                  "n-set",
                                  comparison = "both",
                                  n = 6
                          ),
                          "When choosing: comparison == 'both', the cut.off argument needs to store two cut.off values: lower-cut.off and upper-cut.off"
                  )
          })