context("Test: DiffGenes() ")

data(PhyloExpressionSetExample)

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 DiffGenes()",
          {
                  expect_error(
                          DiffGenes(
                                  ExpressionSet = nonStandardExpressionSet,
                                  nrep          = 2,
                                  comparison    = "below",
                                  method        = "foldchange",
                                  stage.names   = c("S1", "S2", "S3")
                          )
                   )
          })



test_that("Correct fold change values are computed..", {
        set.seed(123)
        ExampleMicroarrayTable <-
                PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
        
        stage.1 <-
                apply(
                        cbind(ExampleMicroarrayTable[, 3], ExampleMicroarrayTable[, 4]) ,
                        1 ,
                        myTAI::geom.mean
                )
        stage.2 <-
                apply(
                        cbind(ExampleMicroarrayTable[, 5], ExampleMicroarrayTable[, 6]) ,
                        1 ,
                        myTAI::geom.mean
                )
        
        
        expect_equal(
                DiffGenes(
                        ExpressionSet = ExampleMicroarrayTable,
                        nrep          = 2,
                        comparison    = "below",
                        method        = "foldchange",
                        stage.names   = c("S1", "S2", "S3")
                )[, 3],
                stage.1 / stage.2
        )
        
})




test_that("Correct log fold change values are computed..", {
        set.seed(123)
        ExampleMicroarrayTable <-
                PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
        
        stage.1 <-
                apply(
                        cbind(ExampleMicroarrayTable[, 3], ExampleMicroarrayTable[, 4]) ,
                        1 ,
                        myTAI::geom.mean
                )
        stage.2 <-
                apply(
                        cbind(ExampleMicroarrayTable[, 5], ExampleMicroarrayTable[, 6]) ,
                        1 ,
                        myTAI::geom.mean
                )
        
        
        expect_equal(
                DiffGenes(
                        ExpressionSet = tf(ExampleMicroarrayTable, log2),
                        nrep          = 2,
                        comparison    = "below",
                        method        = "log-foldchange",
                        stage.names   = c("S1", "S2", "S3")
                )[, 3],
                log2(stage.1) - log2(stage.2)
        )
        
})

test_that("Correct p-values based on the t-test are computed..", {
        set.seed(123)
        ExampleMicroarrayTable <-
                PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
        
        stage.comp <-
                apply(cbind(ExampleMicroarrayTable[, 3:4], ExampleMicroarrayTable[, 5:6]) , 1 , function(x)
                        t.test(x[1:2], x[3:4])$p.value)
        
        
        expect_equal(
                DiffGenes(
                        ExpressionSet = ExampleMicroarrayTable,
                        nrep          = 2,
                        comparison    = "below",
                        method        = "t.test",
                        stage.names   = c("S1", "S2", "S3")
                )[, 3],
                as.numeric(stage.comp)
        )
        
})


test_that("Correct p-values based on the wilcox.test are computed..", {
        set.seed(123)
        ExampleMicroarrayTable <-
                PhyloExpressionSetExample[sample(1:22000, 10) , 1:8]
        
        stage.comp <-
                apply(cbind(ExampleMicroarrayTable[, 3:4], ExampleMicroarrayTable[, 5:6]) , 1 , function(x)
                        wilcox.test(x[1:2], x[3:4])$p.value)
        
        
        expect_equal(
                DiffGenes(
                        ExpressionSet = ExampleMicroarrayTable,
                        nrep          = 2,
                        comparison    = "below",
                        method        = "wilcox.test",
                        stage.names   = c("S1", "S2", "S3")
                )[, 3],
                as.numeric(stage.comp)
        )
        
})