context("Test: CollapseReplicates() ")

# adapted from: https://github.com/hadley/dplyr/blob/master/tests/testthat/test-arrange.r
equal_df <- function(df1, df2) {
        rownames(df1) <- NULL
        rownames(df2) <- NULL
        isTRUE(all.equal(df1, df2))
}

data(PhyloExpressionSetExample)

# test df: mean, nrep = 2, stage.names = c("S1","S2","S3")
TestCollapsedDF1 <-
        cbind(
                PhyloExpressionSetExample[1:5, 1:2],
                apply(PhyloExpressionSetExample[1:5, 3:4], 1, mean),
                apply(PhyloExpressionSetExample[1:5, 5:6], 1, mean),
                apply(PhyloExpressionSetExample[1:5, 7:8], 1, mean)
        )
colnames(TestCollapsedDF1)[3:5] <- c("S1", "S2", "S3")

# test df: mean, nrep = c(2,2,3), stage.names = c("S1","S2","S3")
TestCollapsedDF2 <-
        cbind(
                PhyloExpressionSetExample[1:5, 1:2],
                apply(PhyloExpressionSetExample[1:5, 3:4], 1, mean),
                apply(PhyloExpressionSetExample[1:5, 5:6], 1, mean),
                apply(PhyloExpressionSetExample[1:5, 7:9], 1, mean)
        )
colnames(TestCollapsedDF2)[3:5] <- c("S1", "S2", "S3")

# test df: median, nrep = 2, stage.names = c("S1","S2","S3")
TestCollapsedDF3 <-
        cbind(
                PhyloExpressionSetExample[1:5, 1:2],
                apply(PhyloExpressionSetExample[1:5, 3:4], 1, median),
                apply(PhyloExpressionSetExample[1:5, 5:6], 1, median),
                apply(PhyloExpressionSetExample[1:5, 7:8], 1, median)
        )
colnames(TestCollapsedDF3)[3:5] <- c("S1", "S2", "S3")

# test df: max, nrep = 2, stage.names = c("S1","S2","S3")
TestCollapsedDF4 <-
        cbind(
                PhyloExpressionSetExample[1:5, 1:2],
                apply(PhyloExpressionSetExample[1:5, 3:4], 1, max),
                apply(PhyloExpressionSetExample[1:5, 5:6], 1, max),
                apply(PhyloExpressionSetExample[1:5, 7:8], 1, max)
        )
colnames(TestCollapsedDF4)[3:5] <- c("S1", "S2", "S3")


# test df: median, nrep = c(2,2,3), stage.names = c("S1","S2","S3")
TestCollapsedDF5 <-
        cbind(
                PhyloExpressionSetExample[1:5, 1:2],
                apply(PhyloExpressionSetExample[1:5, 3:4], 1, median),
                apply(PhyloExpressionSetExample[1:5, 5:6], 1, median),
                apply(PhyloExpressionSetExample[1:5, 7:9], 1, median)
        )
colnames(TestCollapsedDF5)[3:5] <- c("S1", "S2", "S3")

# test df: max, nrep = c(2,2,3), stage.names = c("S1","S2","S3")
TestCollapsedDF6 <-
        cbind(
                PhyloExpressionSetExample[1:5, 1:2],
                apply(PhyloExpressionSetExample[1:5, 3:4], 1, max),
                apply(PhyloExpressionSetExample[1:5, 5:6], 1, max),
                apply(PhyloExpressionSetExample[1:5, 7:9], 1, max)
        )
colnames(TestCollapsedDF6)[3:5] <- c("S1", "S2", "S3")


test_that("CollapseReplicates() works with const. nrep = 2 and FUN = mean", {
        expect_true(equal_df(
                CollapseReplicates(
                        PhyloExpressionSetExample[1:5, 1:8],
                        2,
                        mean,
                        c("S1", "S2", "S3")
                ),
                tibble::as_tibble(TestCollapsedDF1)
        ))
        
})

test_that("CollapseReplicates() works with const. nrep = 2 and FUN = 'mean' (quoted)",
          {
                  expect_true(equal_df(
                          CollapseReplicates(
                                  PhyloExpressionSetExample[1:5, 1:8],
                                  2,
                                  "mean",
                                  c("S1", "S2", "S3")
                          ),
                          tibble::as_tibble(TestCollapsedDF1)
                  ))
                  
          })


test_that("CollapseReplicates() works with const. nrep = 2 and FUN = median", {
        expect_true(equal_df(
                CollapseReplicates(
                        PhyloExpressionSetExample[1:5, 1:8],
                        2,
                        median,
                        c("S1", "S2", "S3")
                ),
                tibble::as_tibble(TestCollapsedDF3)
        ))
        
})

test_that("CollapseReplicates() works with const. nrep = 2 and FUN = max", {
        expect_true(equal_df(
                CollapseReplicates(PhyloExpressionSetExample[1:5, 1:8], 2, max, c("S1", "S2", "S3")),
                tibble::as_tibble(TestCollapsedDF4)
        ))
        
})

test_that("CollapseReplicates() works with variable nrep = c(2,2,3) and FUN = mean",
          {
                  expect_true(equal_df(
                          CollapseReplicates(
                                  PhyloExpressionSetExample[1:5, 1:9],
                                  c(2, 2, 3),
                                  mean,
                                  c("S1", "S2", "S3")
                          ),
                          tibble::as_tibble(TestCollapsedDF2)
                  ))
                  
          })


test_that("CollapseReplicates() works with variable nrep = c(2,2,3) and FUN = median",
          {
                  expect_true(equal_df(
                          CollapseReplicates(
                                  PhyloExpressionSetExample[1:5, 1:9],
                                  c(2, 2, 3),
                                  median,
                                  c("S1", "S2", "S3")
                          ),
                          tibble::as_tibble(TestCollapsedDF5)
                  ))
                  
          })

test_that("CollapseReplicates() works with variable nrep = c(2,2,3) and FUN = max",
          {
                  expect_true(equal_df(
                          CollapseReplicates(
                                  PhyloExpressionSetExample[1:5, 1:9],
                                  c(2, 2, 3),
                                  max,
                                  c("S1", "S2", "S3")
                          ),
                          tibble::as_tibble(TestCollapsedDF6)
                  ))
                  
          })

nonStandardExpressionSet <- PhyloExpressionSetExample[, 2:9]

test_that(
        "is.ExpressionSet() throughs error when no ExpressionSet is entered to CollapseReplicates()",
        {
                expect_error(
                        CollapseReplicates(nonStandardExpressionSet, 2, mean)
                        )
        }
)


TestCollapsedDF_stage.names <- TestCollapsedDF1
colnames(TestCollapsedDF_stage.names)[3:5] <- paste0("X", 1:3)

test_that("default stage.names work properly when stage.names = NULL", {
        expect_true(equal_df(
                CollapseReplicates(PhyloExpressionSetExample[1:5, 1:8], 2, mean),
                tibble::as_tibble(TestCollapsedDF_stage.names)
        ))
        
})

test_that("CollapseReplicates() works with single replicates nrep = 1 and FUN = mean", {
        expect_true(equal_df(
                CollapseReplicates(
                        PhyloExpressionSetExample[1:5, 1:5],
                        1,
                        mean,
                        c("Zygote", "Quadrant", "Globular")
                ),
                tibble::as_tibble(PhyloExpressionSetExample[1:5, 1:5])
        ))
        
})