context("Test: pMatrix() ")


data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

equal_df <- function(df1, df2) {
        rownames(df1) <- NULL
        rownames(df2) <- NULL
        isTRUE(all.equal(df1, df2))
}

partialTAI <- function(ExpressionSet) {
        ncols <- ncol(ExpressionSet)
        #s <- colSums(ExpressionSet[ , 3:ncols])
        partialTXI <-
                matrix(NA_real_,
                       nrow = nrow(ExpressionSet),
                       ncol = ncols - 2)
        for (i in 1:(ncols - 2)) {
                partialTXI[, i] <-
                        ExpressionSet[, 1] * (ExpressionSet[, i + 2] / sum(ExpressionSet[, i +
                                                                                                 2]))
        }
        
        colnames(partialTXI) <- colnames(ExpressionSet)[3:ncols]
        rownames(partialTXI) <- ExpressionSet[, 2]
        return(partialTXI)
}


nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

test_that("is.ExpressionSet() throughs error when no ExpressionSet is entered to pMatrix()",
          {
                  expect_error(
                          pMatrix(nonStandardExpressionSet)
                  )
          })


test_that("pMatrix() computes correct partial TAI values ", {
        expect_true(equal_df(
                pMatrix(PhyloExpressionSetExample),
                partialTAI(PhyloExpressionSetExample)
        ))
})

test_that("pMatrix() computes correct partial TDI values ", {
        expect_true(equal_df(
                pMatrix(DivergenceExpressionSetExample),
                partialTAI(DivergenceExpressionSetExample)
        ))
})

test_that("colSums(pMatrix(ExpressionSet)) == TAI(ExpressionSet)", {
        expect_equal(colSums(pMatrix(PhyloExpressionSetExample)), TAI(PhyloExpressionSetExample))
        expect_equal(colSums(pMatrix(DivergenceExpressionSetExample)),
                     TDI(DivergenceExpressionSetExample))
})


test_that("colSums(pMatrix(ExpressionSet)) == colSums(pStrata(ExpressionSet))",
          {
                  expect_equal(colSums(pMatrix(PhyloExpressionSetExample)), colSums(pStrata(PhyloExpressionSetExample)))
                  expect_equal(colSums(pMatrix(DivergenceExpressionSetExample)), colSums(pStrata(DivergenceExpressionSetExample)))
                  
          })