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# Tests the quickSubCluster utility.
# require(scran); require(testthat); source("setup.R"); source("test-subclust.R")
library(scran)
set.seed(30000)
ncells <- 700
ngenes <- 1000
dummy <- matrix(rnbinom(ncells*ngenes, mu=10, size=20), ncol=ncells, nrow=ngenes)
set.seed(30001)
test_that("quickSubCluster's defaults are consistent with quickCluster's defaults", {
output <- quickCluster(dummy, min.size=0)
output2 <- quickSubCluster(dummy, groups=rep(1, ncol(dummy)))
expect_identical(as.character(output), sub(".*\\.", "", output2[[1]]$subcluster))
sampling <- sample(3, ncells, replace=TRUE)
output <- quickSubCluster(dummy, groups=sampling)
for (i in unique(sampling)) {
ref <- quickCluster(dummy[,i==sampling], min.size=0)
expect_identical(as.character(ref), sub(".*\\.", "", output[[i]]$subcluster))
}
})
set.seed(30001)
test_that("quickSubCluster's metadata output makes sense", {
sampling <- sample(3, ncells, replace=TRUE)
output <- quickSubCluster(dummy, groups=sampling)
for (i in unique(sampling)) {
expect_identical(metadata(output)$index[[i]], which(sampling==i))
expect_identical(metadata(output)$subcluster[metadata(output)$index[[i]]], output[[i]]$subcluster)
}
expect_identical(sub("\\..*", "", metadata(output)$subcluster), as.character(sampling))
raw.out <- quickSubCluster(dummy, groups=sampling, simplify=TRUE)
expect_identical(metadata(output)$subcluster, raw.out)
})
set.seed(30002)
test_that("quickSubCluster behaves correctly upon changing the assay", {
dummy <- matrix(rnbinom(ncells*ngenes, mu=10, size=20), ncol=ncells, nrow=ngenes)
sampling <- sample(3, ncells, replace=TRUE)
sce <- SingleCellExperiment(list(whee=dummy, blah=scuttle::normalizeCounts(dummy)))
output <- quickSubCluster(dummy, groups=sampling)
output2 <- quickSubCluster(sce, groups=sampling, assay.type="whee")
expect_identical(lapply(output, reducedDim), lapply(output2, reducedDim))
# Checking that we get the same output when we turn off normalization.
expect_error(output <- quickSubCluster(scuttle::normalizeCounts(dummy), groups=sampling, normalize=FALSE), NA)
output2 <- quickSubCluster(sce, groups=sampling, normalize=FALSE, assay.type="blah")
expect_identical(lapply(output, reducedDim), lapply(output2, reducedDim))
})
set.seed(30003)
test_that("quickSubCluster avoids subclustering with too few cells", {
ncells <- 99
dummy <- matrix(rnbinom(ncells*ngenes, mu=10, size=20), ncol=ncells, nrow=ngenes)
sampling <- sample(2, ncells, replace=TRUE)
suppressWarnings(output <- quickSubCluster(dummy, groups=sampling))
has.sub1 <- any(grepl("\\.", output[[1]]$subcluster))
has.sub2 <- any(grepl("\\.", output[[2]]$subcluster))
expect_true(has.sub1!=has.sub2)
# Avoids crashing with one-cell clusters.
test <- quickSubCluster(dummy, groups=rep(1:2, c(1, ncells-1)))
expect_equivalent(counts(test[[1]]), dummy[,1,drop=FALSE])
})
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