Nothing
test_that("BBKNN works for matrix", {
data("panc8_small")
pca <- Embeddings(panc8_small, reduction = "pca")
b <- panc8_small$dataset
n <- length(unique(b))
k <- 3
bbknn <- RunBBKNN(pca, b, neighbors_within_batch = k, verbose = FALSE)
expect_equal(nrow(bbknn$nn.idx), nrow(pca))
expect_equal(nrow(bbknn$nn.dist), nrow(pca))
expect_equal(ncol(bbknn$nn.idx), k * n)
expect_equal(nrow(bbknn$connectivities), nrow(pca))
expect_equal(ncol(bbknn$connectivities), nrow(pca))
})
test_that("BBKNN works for nndescent", {
data("panc8_small")
pca <- Embeddings(panc8_small, reduction = "pca")
b <- panc8_small$dataset
n <- length(unique(b))
k <- 3
bbknn <- RunBBKNN(
pca, b,
neighbors_within_batch = k,
method = "nndescent",
verbose = FALSE
)
expect_equal(nrow(bbknn$nn.idx), nrow(pca))
expect_equal(nrow(bbknn$nn.dist), nrow(pca))
expect_equal(ncol(bbknn$nn.idx), k * n)
expect_equal(nrow(bbknn$connectivities), nrow(pca))
expect_equal(ncol(bbknn$connectivities), nrow(pca))
})
test_that("BBKNN works for Seurat", {
data("panc8_small")
k <- 3
panc8_small <- RunBBKNN(
panc8_small,
batch_key = "tech",
neighbors_within_batch = k,
method = "nndescent",
verbose = FALSE
)
expect_s4_class(panc8_small[['RNA_bbknn']], "Graph")
expect_s4_class(panc8_small[['RNA.bbknn']], "Neighbor")
expect_s4_class(panc8_small[['umap']], "DimReduc")
expect_s4_class(panc8_small[['tsne']], "DimReduc")
})
test_that("BBKNN returns umap model", {
data("panc8_small")
k <- 3
expect_warning(panc8_small <- RunBBKNN(
panc8_small,
batch_key = "tech",
neighbors_within_batch = k,
method = "nndescent",
return.umap.model = TRUE,
verbose = FALSE
))
expect_true(is.list(Misc(panc8_small[['umap']], "model")))
})
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