tests/testthat/test-validation.R

In theislab/zellkonverter: Conversion Between scRNA-seq Objects

file <- system.file("extdata", "example_anndata.h5ad",
                    package = "zellkonverter")
sce <- readH5AD(file)

names <- list(
    assays = c("X", "counts"),
    colData = "louvain",
    rowData = c("n_counts", "highly_variable", "means", "dispersions",
                "dispersions_norm"),
    metadata = c("louvain", "neighbors", "pca", "rank_genes_groups", "umap"),
    redDim = c("X_pca", "X_umap"),
    varm = "PCs",
    colPairs = c("connectivities", "distances")
)

missing <- list()

test_that("validateH5ADSCE works", {
    validateH5ADSCE(sce, names, missing)
    expect_error(
        validateH5ADSCE(sce, names, list(varm = "PCs")),
        "varm names missing is not TRUE"
    )
})

test_that("expectSCE works", {
    expectSCE(sce, sce)
})