context("Test: pStrata() ")


data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

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

partialStrata <- 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]))
        }
        
        partialStrata <-
                matrix(NA_real_, ncol = ncols - 2, nrow = length(names(table(
                        ExpressionSet[, 1]
                ))))
        for (j in 1:length(names(table(ExpressionSet[, 1])))) {
                partialStrata[j,] <-
                        colSums(partialTXI[which(ExpressionSet[, 1] == j) ,])
        }
        
        colnames(partialStrata) <- colnames(ExpressionSet)[3:ncols]
        rownames(partialStrata) <- names(table(ExpressionSet[, 1]))
        return(partialStrata)
}

nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

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


test_that("pStrata() computes correct partial TAI values ", {
        expect_true(equal_df(
                pStrata(PhyloExpressionSetExample),
                partialStrata(PhyloExpressionSetExample)
        ))
})

test_that("pStrata() computes correct partial TDI values ", {
        expect_true(equal_df(
                pStrata(DivergenceExpressionSetExample),
                partialStrata(DivergenceExpressionSetExample)
        ))
})

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