context("Test: REMatrix() ")

data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

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


TestREMatrix1 <-
        t(apply(dplyr::summarise_all(
                dplyr::group_by(PhyloExpressionSetExample[, c(1, 3:9)], Phylostratum),
                list(mean)
        )[, 2:8], 1, function(x)
                (x - min(x)) / (max(x) - min(x))))
rownames(TestREMatrix1) <- 1:12

TestREMatrix2 <-
        t(apply(dplyr::summarise_all(
                dplyr::group_by(DivergenceExpressionSetExample[, c(1, 3:9)], Divergence.stratum),
                list(mean)
        )[, 2:8], 1, function(x)
                (x - min(x)) / (max(x) - min(x))))
rownames(TestREMatrix2) <- 1:10


nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

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


test_that("REMatrix() computes correct values...", {
        expect_true(equal_df(REMatrix(PhyloExpressionSetExample), TestREMatrix1))
        expect_true(equal_df(
                REMatrix(DivergenceExpressionSetExample),
                TestREMatrix2
        ))
})

test_that("error occurs when when REMatrix() is computed on only one developmental stage ",
          {
                  expect_error(REMatrix(PhyloExpressionSetExample[, 1:3]))
          })