tests/testthat/test-tf.R

In myTAI: Evolutionary Transcriptomics

context("Test : tf() ")

data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

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 tf()",
          {
                  expect_error(
                          tf(nonStandardExpressionSet)
                  )
          })

Test.tf.Func <- function(ExpressionSet, FUN) {
        f <- match.fun(FUN)
        ncols <- ncol(ExpressionSet)
        res <-
                cbind(ExpressionSet[, 1:2], apply(ExpressionSet[, 3:ncols], 2, f))
        return(res)
}

test_that("tf() computes correct transformation values ", {
        expect_true(equal_df(
                tf(PhyloExpressionSetExample , log2),
                Test.tf.Func(PhyloExpressionSetExample, log2)
        ))
        expect_true(equal_df(
                tf(DivergenceExpressionSetExample , log2),
                Test.tf.Func(DivergenceExpressionSetExample, log2)
        ))
        
        expect_true(equal_df(
                tf(PhyloExpressionSetExample , sqrt),
                Test.tf.Func(PhyloExpressionSetExample, sqrt)
        ))
        expect_true(equal_df(
                tf(DivergenceExpressionSetExample , sqrt),
                Test.tf.Func(DivergenceExpressionSetExample, sqrt)
        ))
        
        expect_true(equal_df(
                tf(PhyloExpressionSetExample , log2),
                Test.tf.Func(PhyloExpressionSetExample, log2)
        ))
        expect_true(equal_df(
                tf(DivergenceExpressionSetExample , sqrt),
                Test.tf.Func(DivergenceExpressionSetExample, sqrt)
        ))
        
        expect_true(equal_df(
                tf(PhyloExpressionSetExample , function(x)
                        x / 2),
                Test.tf.Func(PhyloExpressionSetExample, function(x)
                        x / 2)
        ))
        expect_true(equal_df(
                tf(DivergenceExpressionSetExample , function(x)
                        x / 2),
                Test.tf.Func(DivergenceExpressionSetExample, function(x)
                        x / 2)
        ))
})