tests/testthat/test-featureSelection.R

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

# scran_modelGeneVar.R
library(singleCellTK)
context("Testing scran_modelGeneVar.R")
data(scExample, package = "singleCellTK")
sce <- runSeuratNormalizeData(sce)

test_that(desc = "Testing FindHVG", {
    # Running each method
    sce <- runModelGeneVar(sce, "seuratNormData")
    metricNames.mgv <- metadata(sce)$sctk$runFeatureSelection$modelGeneVar$rowData
    testthat::expect_true(all(metricNames.mgv %in% names(rowData(sce))))

    sce <- runFeatureSelection(sce, "counts", "vst")
    metricNames.vst <- metadata(sce)$sctk$runFeatureSelection$vst$rowData
    testthat::expect_true(all(metricNames.vst %in% names(rowData(sce))))

    sce <- runFeatureSelection(sce, "seuratNormData", "dispersion")
    metricNames.disp <- metadata(sce)$sctk$runFeatureSelection$dispersion$rowData
    testthat::expect_true(all(metricNames.disp %in% names(rowData(sce))))

    sce <- runFeatureSelection(sce, "seuratNormData", "mean.var.plot")
    metricNames.mvp <- metadata(sce)$sctk$runFeatureSelection$mean.var.plot$rowData
    testthat::expect_true(all(metricNames.mvp %in% names(rowData(sce))))

    # Test accessor functions
    sce <- setTopHVG(sce, "modelGeneVar", hvgNumber = 50, altExp = TRUE, featureSubsetName = NULL)
    #sce <- setTopHVG(sce, "modelGeneVar", hvgNumber = 2000, altExp = TRUE, featureSubsetName = NULL)
    nHVG <- length(getTopHVG(sce, hvgNumber = 50, useFeatureSubset = "HVG_modelGeneVar50"))
    
    testthat::expect_true(is.logical(rowData(sce)$HVG_modelGeneVar50))
    testthat::expect_equal(nrow(altExp(sce, "HVG_modelGeneVar50")), nHVG)
    testthat::expect_equal(metadata(sce)$sctk$featureSubsets$HVG_modelGeneVar50$useAssay,
                           "seuratNormData")

    hvgs <- getTopHVG(sce, "mean.var.plot", hvgNumber = 2000,
                      featureDisplay = "feature_name", useFeatureSubset = NULL)
    testthat::expect_false(all(startsWith(hvgs, "ENSG00000")))
    hvgs <- getTopHVG(sce, "vst", hvgNumber = 2000, useFeatureSubset = NULL)
    vm1 <- plotTopHVG(sce, "dispersion", hvgNumber = NULL)
    vm2 <- plotTopHVG(sce, "modelGeneVar", hvgNumber = 30, labelsCount = 10,
                     featureDisplay = "feature_name")
    vm3 <- plotTopHVG(sce, method = "mean.var.plot",
                      useFeatureSubset = "HVG_modelGeneVar50", hvgNumber = NULL)
    testthat::expect_true(inherits(vm1, "ggplot"))
    testthat::expect_true(inherits(vm2, "ggplot"))
    testthat::expect_true(inherits(vm3, "ggplot"))
})