# Setup library(CRMetrics) library(magrittr) library(Matrix) # Simulate data set.seed(123) testdata.cms <- lapply(seq_len(4), \(x) { out <- rsparsematrix(1e4, 3e3, 0.1) out[out < 0] <- 1 dimnames(out) <- list(sapply(1:1e4, \(x) paste0("gene",x)), sapply(1:3e3, \(x) paste0("cell",x))) return(out) }) %>% setNames(c("sample1","sample2","sample3","sample4")) # Initialize and add summary crm <- CRMetrics$new(cms = testdata.cms, n.cores = 1) # Tests test_that("Check metadata object", { expect_equal(nrow(crm$metadata), 4) }) crm$addComparison("sample") test_that("Check comparison group", { expect_equal(crm$comp.group, "sample") }) test_that("Check preprocessing", { skip_if_not_installed("pagoda2") crm$doPreprocessing(min.transcripts.per.cell = 0, min.cells.per.gene = 0) expect_equal(length(crm$cms.preprocessed), 4) }) test_that("Check embedding object", { skip_if_not_installed("pagoda2") skip_if_not_installed("conos") crm$createEmbedding(arg.embedGraph = list(method = "largeVis")) expect_equal(nrow(crm$con$embedding), 1.2e4) }) test_that("Check depth vector", { crm$getDepth() expect_equal(length(crm$getDepth()), 1.2e4) })