tests/testthat/test-RSEC.R

In clusterExperiment: Compare Clusterings for Single-Cell Sequencing

context("RSEC")
seedValue<-495 #01875 works for sample.kind="Rejection"
test_that("`RSEC` works with matrix, ClusterExperiment, summarizedExperiment",{
	## these examples don't do dendrogram/merge because all -1 after makeConsensus
	## only tests clusterMany, makeConsensus parts.
	## so can't do expect_silent, because returns NOTE about that issue.
	expect_message(rsecOut1<-RSEC(x=mat, isCount=FALSE,reduceMethod="none",k0s=4:5,
		clusterFunction="tight", alphas=0.1,dendroReduce="none",
        subsampleArgs=list(resamp.num=5),random.seed=seedValue
  	 	),"makeDendrogram encountered following error")
   expect_message(rsecOut2<-RSEC(x=cc, reduceMethod="none",k0s=4:5,
   		clusterFunction="tight", alphas=0.1,dendroReduce="none",
       subsampleArgs=list(resamp.num=5),random.seed=seedValue
  	 	),"makeDendrogram encountered following error")
  expect_message(rsecOut3<-RSEC(x=ccSE,
	  reduceMethod="none",k0s=4:5,clusterFunction="tight", 
	  alphas=0.1,dendroReduce="none",
       subsampleArgs=list(resamp.num=5),random.seed=seedValue),
	   "makeDendrogram encountered following error")
   expect_message(rsecOut4<-RSEC(x=se,isCount=FALSE,reduceMethod="none",
   		k0s=4:5,clusterFunction="tight", alphas=0.1,dendroReduce="none",
       subsampleArgs=list(resamp.num=5),random.seed=seedValue),
	   "makeDendrogram encountered following error")
	   #test rerunClusterMany argument:
	expect_message(rsecOut5<-RSEC(rsecOut2,reduceMethod="none",
		k0s=4:5,clusterFunction="tight", alphas=0.1,dendroReduce="none",rerunClusterMany=TRUE,
		subsampleArgs=list(resamp.num=5),random.seed=seedValue),
		"makeDendrogram encountered following error")
    #makes dendrogram so important have here so has to catch defaults of RSEC...
	expect_message(rsecOut6<-RSEC(rsecOut2,
			reduceMethod="none",k0s=4:5,clusterFunction="tight", 
			alphas=0.1,dendroReduce="none",rerunClusterMany=FALSE,
			subsampleArgs=list(resamp.num=5),random.seed=seedValue),
			"makeDendrogram encountered following error")
})

test_that("`RSEC` works through whole series of steps",{
    skip_on_os("windows")
#bigger example where actually goes through all the steps, takes some time:
    expect_message(rsecOut<-RSEC(
        x=assay(seSimCount), isCount=TRUE,reduceMethod="none",
        k0s=4:5,clusterFunction="hierarchical01", alphas=0.1, 
        betas=0.9,minSizes=1,
        subsampleArgs=list(resamp.num=5), seqArgs=list(top.can=0),
        random.seed=seedValue, makeMissingDiss=TRUE,
        consensusProportion=0.7, consensusMinSize=5,
        dendroReduce="none", stopOnErrors = FALSE,
        mergeMethod = "adjP", 
        mergeDEMethod="edgeR",mergeCutoff = 0.05),
        "Merging will be done on")
    expect_silent(ceOut<- clusterMany(x=assay(seSimCount), isCount=TRUE,
        reduceMethod="none", 
        ks=4:5, clusterFunction="hierarchical01", alphas=0.1, 
        betas=0.9, minSizes=1,
        transFun = NULL,
        sequential=TRUE,removeSil=FALSE,subsample=TRUE,
        silCutoff=0,distFunction=NA,
        nFilterDims=NA,nReducedDims=NA,
        mainClusterArgs=NULL,subsampleArgs=list(resamp.num=5),
        ncores=1,run=TRUE, verbose=FALSE,stopOnErrors = TRUE,
        seqArgs=list(verbose=FALSE,top.can=0),random.seed=seedValue
        ))
	expect_equal(clusterMatrix(rsecOut,
        whichClusters="clusterMany"),clusterMatrix(ceOut))
    expect_message(combOut<-makeConsensus(ceOut, 
        proportion = 0.7,minSize = 5),
        "no clusters specified to combine")
    expect_equal(clusterMatrix(rsecOut,
            whichClusters="makeConsensus"),
        clusterMatrix(combOut,
            whichClusters="makeConsensus"))
    expect_equal(clusterMatrix(rsecOut,which=coClustering(rsecOut)),
        clusterMatrix(combOut,which=coClustering(combOut)))

    expect_silent(dendOut<-makeDendrogram(combOut,
        reduceMethod="none",nDims=NA))
    #they differ in tdata:
    expect_equal(as(dendOut@dendro_clusters,"phylo4"), 
        as(rsecOut@dendro_clusters,"phylo4"))
    tdRsec<-phylobase::tdata(rsecOut@dendro_clusters)
    tdRsec<-tdRsec[,-grep("ClusterIdMerge",colnames(tdRsec))]
    td<-phylobase::tdata(dendOut@dendro_clusters)
    td<-td[,-grep("ClusterIdMerge",colnames(td))]
    expect_equal(td, tdRsec)
    expect_equal(clusterExperiment:::.hasOutBranch(dendOut),
        clusterExperiment:::.hasOutBranch(rsecOut))
 #now should be the same, check all objects except dendro_samples because very big:
    expect_message(mergeOut<-mergeClusters(dendOut,mergeMethod = "adjP", 
        DEMethod="edgeR",cutoff = 0.05),
        "Merging will be done on")
    expect_equal(dendroClusterIndex(mergeOut),dendroClusterIndex(rsecOut))
    expect_equal(mergeOut@dendro_clusters,rsecOut@dendro_clusters)
    expect_equal(clusterExperiment:::.hasOutBranch(mergeOut),
        clusterExperiment:::.hasOutBranch(rsecOut))
    expect_equal(coClustering(mergeOut),coClustering(rsecOut))
    expect_equal(clusterMatrix(rsecOut,whichClusters="mergeClusters"),
         clusterMatrix(mergeOut,whichClusters="mergeClusters"))
    expect_equal(clusterTypes(rsecOut),clusterTypes(mergeOut))
})

test_that("`RSEC` works with no merging",{
  #do the same, only don't do merging:
    expect_message(rsecOut<-RSEC(x=assay(seSimCount), 
        isCount=TRUE,reduceMethod="none",
        k0s=4:5,clusterFunction="hierarchical01", alphas=0.1,
        betas=0.9,dendroReduce="none",minSizes=1,
        seqArgs=list(top.can=0),
        subsampleArgs=list(resamp.num=5),random.seed=seedValue,
        mergeMethod="none"),
        "clusters will not be merged because argument")
})

test_that("`RSEC` returns clusterMany even when errors later",{
	#error in makeConsensus param
	expect_message(rsecOut1<-
        RSEC(x=mat, isCount=FALSE,k0s=4:5,
		clusterFunction="tight", alphas=0.1, nReducedDims=3,
        subsampleArgs=list(resamp.num=5),random.seed=seedValue, 
        consensusProportion = -1, consensusMinSize = 5),
        "Invalid value for the 'proportion' parameter"
  	 	)
	expect_true("clusterMany" %in% clusterTypes(rsecOut1))

	#error in dendro param
	expect_message(rsecOut2<-RSEC(x=mat, isCount=FALSE,k0s=4:5,
		clusterFunction="tight", alphas=0.1, nReducedDims=3,
        subsampleArgs=list(resamp.num=5),random.seed=seedValue, 
		dendroReduce="myfakemethod"
  	 	),"does not contain the given 'reduceMethod' value")
    expect_true(all(c("clusterMany","makeConsensus") 
        %in% clusterTypes(rsecOut2)))
	
	# error in merging -- give wrong method
    # have to get dataset where can actually make dendrogram... 
    # takes longer.
    # > sample(size=50,x=1:nrow(seSimCount))
#      [1]  67  47  34 124  23  40 104  93  18  26 123  77  64  35  90  58 103 153  62  66 138  57 118  50  60 145  52 134  45  78  12
#     [32]  38 121  63 128 111 117  56  43  51 149   9  73 150   6  39 125 133 127 152
    set.seed(4289)
	expect_message(rsecOut3<-RSEC(x=
        assay(seSimCount[sample(size=50,x=1:nrow(seSimCount)),]), 
        isCount=TRUE,reduceMethod="none",
        k0s=4:5,clusterFunction="pam", alphas=0.1,
        betas=0.9,dendroReduce="none",minSizes=1,
        subsampleArgs=list(resamp.num=5,clusterFunction="kmeans"),
        random.seed=seedValue,
		mergeMethod="fakeMerge"
  	 	),"mergeClusters encountered following error")

    expect_true(all(c("clusterMany","makeConsensus") %in% clusterTypes(rsecOut3)))

})

test_that("`RSEC` works with hdf5",{

	skip_on_os("windows")

	expect_message(rsecOut2<-RSEC(hdfObj, isCount=FALSE,k0s=4:5,
        reduceMethod="PCA",
		clusterFunction="hierarchical01", alphas=0.1, nReducedDims=3,
        subsampleArgs=list(resamp.num=5),
        seqArgs=list(top.can=0),
        random.seed=seedValue),
		"Merging will be done on"
		)

	expect_message(rsecOut3<-RSEC(assay(hdfObj), isCount=FALSE,
        k0s=4:5, reduceMethod="PCA",
		clusterFunction="hierarchical01", alphas=0.1, nReducedDims=3,
	    subsampleArgs=list(resamp.num=5),
        seqArgs=list(top.can=0), random.seed=seedValue),
		"Merging will be done on"
		)

	expect_equal(clusterMatrix(rsecOut2),clusterMatrix(rsecOut3))
	
	#no reduce method, do everything on raw data
    #requires numeric/complex matrix/vector arguments
	expect_message(rsecOut1<-RSEC(hdfObj, isCount=FALSE,
        k0s=4:5,reduceMethod="none",
		clusterFunction="hierarchical01", alphas=0.1, 
        seqArgs=list(top.can=0), 
        subsampleArgs=list(resamp.num=5,clusterFunction="pam"),
        random.seed=seedValue),
		"Merging will be done on"
		)
})

test_that("`RSEC` passing args to subsample",{
    #test in passing to subsampleArgs
  	expect_message(rsecOut1<-RSEC(x=mat, 
  				   isCount=FALSE,reduceMethod="none",k0s=4:5,
  	               clusterFunction="tight", alphas=0.1,dendroReduce="none",
  	               subsampleArgs=list(resamp.num=5),random.seed=495),
  				   "makeDendrogram encountered following error")
  	expect_message(rsecOut2<-RSEC(x=mat, 
  				   isCount=FALSE,reduceMethod="none",k0s=4:5,
  	               clusterFunction="tight", alphas=0.1,dendroReduce="none",
  	               subsampleArgs=list(resamp.num=5),random.seed=495),
  				   "makeDendrogram encountered following error")
  	expect_identical(clusterMatrix(rsecOut1),clusterMatrix(rsecOut2))
    
})