tests/testthat/test-assays.R

In clusterExperiment: Compare Clusterings for Single-Cell Sequencing

context("Assays")

## Construct ClusterExperiment with multiple named assays
multi_se <- SummarizedExperiment(assays = list(counts = simCount,
                                               logcounts = log1p(simCount)))
multi_cc <- ClusterExperiment(multi_se, trueCluster)
ccTrue <- ClusterExperiment(simCount, trueCluster)
ccTrue2 <- ClusterExperiment(simCount, trueCluster, transformation = log1p)
seedValue<-495 #01875 works for sample.kind="Rejection"

test_that("clusterSingle works with non defalt assays", {

    ###Apply to SE
    expect_silent(cl1 <- clusterSingle(multi_se, 
      whichAssay = "counts",
      mainClusterArgs=list(clusterArgs=list(k=3),
          clusterFunction="pam"), 
      subsample=FALSE, sequential=FALSE))

    ###Apply to CE
    expect_silent(cl2 <- clusterSingle(multi_cc, 
        whichAssay = "counts",
        mainClusterArgs=list(clusterArgs=list(k=3), 
            clusterFunction="pam"), 
        subsample=FALSE, 
        sequential=FALSE)
    )

    expect_equal(primaryCluster(cl1), primaryCluster(cl2))


    expect_silent(cl3 <- clusterSingle(multi_cc, 
        whichAssay = "logcounts", 
        mainClusterArgs=list(clusterArgs=list(k=3),
            clusterFunction="pam"),
        subsample=FALSE, sequential=FALSE))

    expect_false(all(primaryCluster(cl2) == primaryCluster(cl3)))

    expect_error(clusterSingle(multi_cc, whichAssay = "normalized",
        mainClusterArgs=list(clusterArgs=list(k=3),
            clusterFunction="pam"),
        subsample=FALSE, sequential=FALSE),
        "'normalized' not in names")

    expect_error(clusterSingle(multi_cc, whichAssay = 3,
        mainClusterArgs=list(clusterArgs=list(k=3),
            clusterFunction="pam"),
        subsample=FALSE, sequential=FALSE),
        "subscript is out of bounds")

})

test_that("clusterMany works with non default assays", {
  expect_silent(cl1 <- clusterMany(multi_cc, ks=c(3,4),clusterFunction="pam",
                                   subsample=FALSE, sequential=FALSE,
                                   whichAssay = "counts",verbose=FALSE))

  expect_silent(cl2 <- clusterMany(multi_se, ks=c(3,4),clusterFunction="pam",
                                   subsample=FALSE, sequential=FALSE,
                                   whichAssay = "counts",verbose=FALSE))

  expect_equal(primaryCluster(cl1), primaryCluster(cl2))


  expect_silent(cl3 <- clusterMany(multi_cc, ks=c(3,4),clusterFunction="pam",
                                   subsample=FALSE, sequential=FALSE,
                                   whichAssay = "logcounts",verbose=FALSE))

  expect_false(all(primaryCluster(cl1) == primaryCluster(cl3)))
})

test_that("mergeClusters works with non default assays", {

  expect_silent(cl2 <- clusterSingle(multi_cc, whichAssay = "counts",
                                     mainClusterArgs=list(clusterArgs=list(k=3),clusterFunction="pam"),
                                     subsample=FALSE, sequential=FALSE))

  expect_silent(cl3 <- clusterSingle(multi_cc, whichAssay = "logcounts",
                                     mainClusterArgs=list(clusterArgs=list(k=3),clusterFunction="pam"),
                                     subsample=FALSE, sequential=FALSE))

  expect_silent(cl3 <- makeDendrogram(cl3, whichAssay = "logcounts"))
  expect_message(merged <- mergeClusters(x=cl3, whichAssay = "logcounts",DEMethod="limma"),
                 "Merging will be done on")

})

test_that("plotting works wih non default assays", {
  expect_silent(plotFeatureBoxplot(object=multi_cc,feature=1,whichAssay=1))
  expect_silent(plotFeatureBoxplot(object=multi_cc,feature=1,whichAssay=2))

  small_cc <- multi_cc[1:10,c(1:3, 290:293)]
  small_cc <- makeDendrogram(small_cc)
  expect_silent(plotHeatmap(small_cc, whichAssay=1))
  expect_silent(plotHeatmap(small_cc, whichAssay=2))

})

test_that("RSEC works wih non default assays", {
    skip_on_os("windows")
    expect_message(out1<-RSEC(x=multi_cc, reduceMethod="none",
        k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
        betas=0.9, dendroReduce="none", minSizes=1,
        subsampleArgs=list(resamp.num=5),   
        seqArgs=list(top.can=0),
        random.seed=seedValue, whichAssay = "counts"),
        "Merging will be done on")

    expect_message(out2<-RSEC(x=multi_cc, reduceMethod="none",
        k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
        betas=0.9, dendroReduce="none", minSizes=1,
        subsampleArgs=list(resamp.num=5),
        seqArgs=list(top.can=0),
        random.seed=seedValue, whichAssay = "logcounts"),
        "Merging will be done on")

    expect_message(out3<-RSEC(x=ccTrue, reduceMethod="none",
        k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
        betas=0.9, dendroReduce="none", minSizes=1,
        subsampleArgs=list(resamp.num=5),
        seqArgs=list(top.can=0),
        random.seed=seedValue),
        "Merging will be done on")

    expect_message(out4<-RSEC(x=ccTrue2, reduceMethod="none",
        k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
        betas=0.9, dendroReduce="none", minSizes=1,
        subsampleArgs=list(resamp.num=5),
        seqArgs=list(top.can=0),
        random.seed=seedValue),
        "Merging will be done on")

    expect_false(all(primaryCluster(out1) == primaryCluster(out2)))

    expect_equivalent(out1, out3)
    expect_equivalent(out2, out4)
})

test_that("RSEC works independent of assay order", {
    skip_on_os("windows")
    #create two with different order of the assays
    multi_se <- SummarizedExperiment(assays = list(counts = simCount,
                                                 logcounts = log1p(simCount)))
    multi_se2 <- SummarizedExperiment(assays = list(logcounts = log1p(simCount),
                                                  counts = simCount))
    multi_cc <- ClusterExperiment(multi_se, trueCluster)
    multi_cc2 <- ClusterExperiment(multi_se2, trueCluster)

    #use character, logcounts on both 
    expect_message(out1<-RSEC(x=multi_cc, reduceMethod="none",
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = "logcounts"),
                 "Merging will be done on")

    expect_message(out2<-RSEC(x=multi_cc2, reduceMethod="none",
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = "logcounts"),
                 "Merging will be done on")

    # had to change the tests, because with new version of bioconductor, order of assays being different is caught, and for some reason wasn't caught before. Very strange passed previously.
    # Want to test everything same but assays
    out1@assays<-out2@assays
    expect_equal(out1, out2)

    #use numeric
    expect_message(out1<-RSEC(x=multi_cc, reduceMethod="none",
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = 2),
                 "Merging will be done on")

    expect_message(out2<-RSEC(x=multi_cc2, reduceMethod="none",
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = 1),
                 "Merging will be done on")
    # Want to test everything same but assays
    out1@assays<-out2@assays
    expect_equal(out1, out2)

    #use character, counts on both with PCA reduce
    # In 2.7.2-9001 had to change this to 60 dims -- no longer ran, probably because changed the clustering slightly?
    expect_message(out1<-RSEC(x=multi_cc, reduceMethod="PCA", nReducedDims = 60,
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5, clusterFunction="pam"),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = "counts"),
                 "Merging will be done on")

    expect_message(out2<-RSEC(x=multi_cc2, reduceMethod="PCA", nReducedDims = 60,
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5, clusterFunction="pam"),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = "counts"),
                 "Merging will be done on")

    # Want to test everything same but assays
    out1@assays<-out2@assays
    expect_equal(out1, out2)

    #use character, counts on both with var reduce
    expect_message(out1<-RSEC(x=multi_cc, reduceMethod="var",
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = "logcounts"),
                 "Merging will be done on")

    expect_message(out2<-RSEC(x=multi_cc2, reduceMethod="var",
                            k0s=4:5, clusterFunction="hierarchical01", alphas=0.1,
                            betas=0.9, dendroReduce="none", minSizes=1,
                            subsampleArgs=list(resamp.num=5),
                            seqArgs=list(top.can=0),
                            random.seed=seedValue, whichAssay = "logcounts"),
                 "Merging will be done on")

    # Want to test everything same but assays
    out1@assays<-out2@assays
    expect_equal(out1, out2)

})