context('Test main Harmony integration function: RunHarmony')
library(harmony)
data(cell_lines_small)

obj <- RunHarmony(cell_lines_small$scaled_pcs, cell_lines_small$meta_data, 'dataset',
                  theta = 1, nclust = 50, lambda = .1, max_iter = 5, return_object = TRUE,
                  verbose = FALSE, .options = harmony_options(max.iter.cluster = 10))

test_that('dimensions match in Harmony object data structures', {
    expect_equal(dim(obj$Y), c(obj$d, obj$K))
    expect_equal(dim(obj$Z_corr), c(obj$d, obj$N))
    expect_equal(dim(obj$Z_cos), c(obj$d, obj$N))
    expect_equal(dim(obj$R), c(obj$K, obj$N))
})

test_that('R defines proper probability distributions', {
    expect_gte(min(obj$R), 0)
    expect_lte(max(obj$R), 1)
    expect_equal(colSums(obj$R), rep(1, obj$N))
})

test_that('there are no null values in the corrected embedding', {
    expect_true(all(!is.infinite(obj$Z_corr)))
    expect_true(all(!is.na(obj$Z_corr)))
    expect_true(all(!is.infinite(obj$Z_cos)))
    expect_true(all(!is.na(obj$Z_cos)))
})


test_that('increasing theta decreases chi2 between Cluster and Batch assign', {
    obj0 <- RunHarmony(cell_lines_small$scaled_pcs, cell_lines_small$meta_data, 'dataset',
                       theta = 0, nclust = 20, lambda = .1, max_iter = 2, return_object = TRUE,
                       verbose = FALSE, .options = harmony_options(max.iter.cluster = 5))
    obj1 <- RunHarmony(cell_lines_small$scaled_pcs, cell_lines_small$meta_data, 'dataset',
                       theta = 1, nclust = 20, lambda = .1, max_iter = 2, return_object = TRUE,
                       verbose = FALSE, .options = harmony_options(max.iter.cluster = 5))

    expect_gt(
        sum(((obj0$O - obj0$E) ^ 2) / obj0$E),
        sum(((obj1$O - obj1$E) ^ 2) / obj1$E)
    )
})

test_that('error messages work', {
    expect_error(
        RunHarmony(cell_lines_small$scaled_pcs, cell_lines_small$meta_data, 'fake_variable')
    )

    expect_error(
        RunHarmony(cell_lines_small$scaled_pcs, cell_lines_small$meta_data, 'dataset', lambda = c(1,2))
    )

    expect_error(
        RunHarmony(cell_lines_small$scaled_pcs, head(cell_lines_small$meta_data, -1), 'dataset')
    )

})