Nothing
tests/testthat/test-mergeClusters.R
In clusterExperiment: Compare Clusterings for Single-Cell Sequencing
context("mergeClusters")
test_that("`mergeClusters` works with matrix",{
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam", clusterArgs=list(k=6)),
isCount=FALSE))
expect_silent(clustWithDendro <- makeDendrogram(cl1))
#matrix version
expect_silent(mergedList <- mergeClusters(x=transformData(cl1), DEMethod="limma", cl=primaryCluster(cl1), dendro=clustWithDendro@dendro_clusters, mergeMethod="adjP", plotInfo="mergeMethod"))
})
test_that("`mergeClusters` works with ClusterExperiment objects", {
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
leg<-clusterLegend(cl1)[[primaryClusterIndex(cl1)]]
leg[,"name"]<-letters[1:6]
clusterLegend(cl1)[[primaryClusterIndex(cl1)]]<-leg
expect_silent(clustWithDendro <- makeDendrogram(cl1))
#check plotting types:
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none",plotInfo="all"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="adjP"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="locfdr"),"Note: Merging will be done on")
expect_warning(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="locfdr",showWarnings=TRUE))
expect_error(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="mergeMethod"),
"can only plot 'mergeMethod' results if one method is selected")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP",
DEMethod="limma", plotInfo="none"),"Note: Merging will be done on")
#check all methods run
for(method in clusterExperiment:::.availMergeMethods){
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod=method, plotInfo="mergeMethod"),"Note: Merging will be done on")
}
expect_true("mergeClusters" %in% clusterTypes(clustMerged))
expect_true("mergeClusters" %in% colnames(clusterMatrix(clustMerged)))
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma",
plotInfo="mergeMethod",leafType="samples",plotType="colorblock"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="samples",plotType="name"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="clusters",plotType="colorblock"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="clusters",plotType="name"),"Note: Merging will be done on")
expect_error(mergeClusters(x=transformData(clustWithDendro), DEMethod="limma",
cl=primaryCluster(clustWithDendro),plot="none",
mergeMethod="adjP",
dendro=clustWithDendro@dendro_samples),
"Not a valid input dendrogram")
expect_error(mergeClusters(clustWithDendro, mergeMethod="adjP"),'argument "DEMethod" is missing, with no default')
#test when merge already exists
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma"),"Merging will be done on")
expect_silent(primaryClusterIndex(clustMerged)<-2)
expect_silent(clustMerged<- makeDendrogram(clustMerged))
expect_message(clustMerged2<-mergeClusters(clustMerged,mergeMethod="adjP"),"Merging will be done on")
expect_true("mergeClusters.1" %in% clusterTypes(clustMerged2))
expect_true(!"makeConsensus.1" %in% clusterTypes(clustMerged2))
expect_true(!"clusterMany.1" %in% clusterTypes(clustMerged2))
expect_silent(removeClusterings(clustMerged, whichClusters = "mergeClusters"))
})
test_that("`mergeClusters` works with HDF5 assay slot",{
expect_silent(cl1 <- clusterSingle(hdfObj,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
expect_silent(clustWithDendro <- makeDendrogram(cl1))
expect_message(mergedCE <- mergeClusters(x=clustWithDendro,plot=FALSE,
mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod"),
"Merging will be done on")
expect_true(inherits(assay(mergedCE),"DelayedArray"))
})
test_that("saving merge info works",{
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE, reduceMethod="none",
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
#check cluster is same, otherwise won't get same results...
expect_equal(primaryCluster(cl1),c(4,1,1,5,1,2,5,1,1,3,3,3,6,6,4,2,2,2))
#for some reason, clusterSingle not giving reasonable names
expect_silent(clustWithDendro <- makeDendrogram(cl1,reduceMethod="none"))
#Dendrogram:
# --[dendrogram w/ 2 branches and 6 members at h = 1509]
# |--leaf "3"
# `--[dendrogram w/ 2 branches and 5 members at h = 1455]
# |--[dendrogram w/ 2 branches and 2 members at h = 228]
# | |--leaf "1"
# | `--leaf "5"
# `--[dendrogram w/ 2 branches and 3 members at h = 337]
# |--leaf "6"
# `--[dendrogram w/ 2 branches and 2 members at h = 259]
# |--leaf "2"
# `--leaf "4"
#matrix version
expect_silent(mergedList <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", plotInfo="none"))
##check giving nodePropTable
expect_message(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="none"),
"Using existing results of per-node significance")
expect_equal(mergedList2$nodeProp[,"adjP"],mergedList$nodeProp[,"adjP"])
expect_silent(mergedListStorey<-mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="mergeMethod"))
expect_equal(mergedList2$nodeProp[,"Storey"],mergedListStorey$nodeProp[,"Storey"])
expect_message(mergedList2Redo<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList2$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="none", plotInfo=c("all")),"Using existing results of per-node significance")
#------
#on ClusterExperiment
# note need to specify message to see doing it correctly.
#------
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",plotInfo="none",plot=FALSE,calculateAll=FALSE),"Merging will be done on")
expect_equal(clustMerged@merge_dendrocluster_index,clustWithDendro@dendro_index+1)
expect_equal(clustMerged@merge_dendrocluster_index,clustMerged@dendro_index)
expect_equal(clustMerged@merge_index,1)
#add to existing with different method
expect_message(clustMerged2 <- mergeClusters(clustMerged, mergeMethod="Storey",
plotInfo="none",cutoff=0.1,plot=FALSE,calculateAll=FALSE),"Merging will be done on")
expect_equal(clustMerged2@merge_dendrocluster_index,clustMerged@dendro_index+1)
expect_equal(clustMerged2@merge_dendrocluster_index,clustMerged2@dendro_index)
expect_equal(clustMerged2@merge_index,1)
#rerun previous with different cutoff -- no new calculations
expect_message(clustMerged3 <- mergeClusters(clustMerged2,mergeMethod="Storey",
plotInfo="none",cutoff=0.05,plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_equal(clustMerged3@merge_dendrocluster_index,clustMerged2@dendro_index+1)
expect_equal(clustMerged3@merge_dendrocluster_index,clustMerged3@dendro_index)
expect_equal(clustMerged3@merge_index,1)
#do it again with higher value that actually merges -- check correct index updates, etc...
expect_message(clustMerged4 <- mergeClusters(clustMerged3,mergeMethod="Storey",
plotInfo="none",cutoff=0.5,plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_equal(clustMerged4@merge_dendrocluster_index,clustMerged3@dendro_index+1)
expect_equal(clustMerged4@merge_dendrocluster_index,clustMerged4@dendro_index)
expect_equal(clustMerged4@merge_index,1)
expect_equal(clustMerged4@merge_nodeMerge[,"mergeClusterId"],c(NA,NA,1,3,NA))
expect_equal(clustMerged4@merge_nodeMerge[,"isMerged"],c(FALSE,FALSE,TRUE,TRUE,TRUE))
# > clustMerged4@merge_nodeMerge
# Node Contrast isMerged mergeClusterId
# Node1 Node1 X3-(X1+X5+X6+X2+X4)/5 FALSE NA
# Node2 Node2 (X1+X5)/2-(X6+X2+X4)/3 FALSE NA
# Node3 Node3 X1-X5 TRUE 1
# Node4 Node4 X6-(X2+X4)/2 TRUE 3
# Node5 Node5 X2-X4 TRUE NA
# > clustMerged4@merge_nodeProp
# Node Contrast Storey PC adjP locfdr MB JC
# Node1 Node1 X3-(X1+X5+X6+X2+X4)/5 1.0 NA 0.55 NA NA NA
# Node2 Node2 (X1+X5)/2-(X6+X2+X4)/3 1.0 NA 0.75 NA NA NA
# Node3 Node3 X1-X5 0.0 NA 0.10 NA NA NA
# Node4 Node4 X6-(X2+X4)/2 0.1 NA 0.15 NA NA NA
# Node5 Node5 X2-X4 0.4 NA 0.00 NA NA NA
# > clustMerged4@merge_nodeMerge
# NodeId Contrast isMerged mergeClusterId
# InternalNodeId7 InternalNodeId7 X3-(X1+X5+X6+X2+X4)/5 FALSE NA
# InternalNodeId8 InternalNodeId8 (X1+X5)/2-(X6+X2+X4)/3 FALSE NA
# InternalNodeId9 InternalNodeId9 X1-X5 TRUE 1
# InternalNodeId10 InternalNodeId10 X6-(X2+X4)/2 TRUE 3
# InternalNodeId11 InternalNodeId11 X2-X4 TRUE NA
#
#check really gets clusterIds and not names
expect_silent(clusterLegend(clustMerged3)[["clusterSingle"]][,"name"]<-letters[1:6])
expect_message(clustMerged5 <- mergeClusters(clustMerged3, mergeMethod="Storey",
plotInfo="none",cutoff=0.5,plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_equal(clustMerged4@merge_nodeMerge,clustMerged5@merge_nodeMerge)
#helpful for debugging:
# plotDendrogram(clustMerged,show.node=TRUE,show.tip.label=TRUE)
# table(clusterMatrix(clustMerged)[,c(1)],clusterMatrix(clustMerged)[,c(2)])
expect_silent(nodeMergeInfo(clustMerged4))
expect_equal(mergeClusterIndex(clustMerged4),clustMerged4@merge_index)
expect_equal(mergeCutoff(clustMerged4),0.5)
expect_equal(mergeMethod(clustMerged4),"Storey")
#check if can calculate all, but do nothing else
expect_message(clustMergedAll<-mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none",plotInfo="none",cutoff=0.5,plot=FALSE,
calculateAll=TRUE),"Merging will be done on")
expect_false(is.na(clustMergedAll@merge_dendrocluster_index))
expect_true(is.na(clustMergedAll@merge_index))
expect_false(is.null(nodeMergeInfo(clustMergedAll)))
#should erase merge info if call dendrogram
expect_silent(clustMergedErase<-makeDendrogram(clustMerged5))
expect_true(is.na(clustMergedErase@merge_index))
expect_true(is.na(clustMergedErase@merge_dendrocluster_index))
#should erase merge info if call dendrogram
expect_silent(clustMergedErase2<-makeDendrogram(clustMergedAll))
expect_true(is.na(clustMergedErase2@merge_index))
expect_true(is.na(clustMergedErase2@merge_dendrocluster_index))
#test getMergeCorresp
#node clustMerge
mgCl<-clusterMatrix(clustMerged)[,clustMerged@merge_index]
ogCl<-clusterMatrix(clustMerged)[,clustMerged@merge_dendrocluster_index]
expect_silent(mc<-getMergeCorrespond(clustMerged))
expect_equal(length(mc),length(unique(mgCl[mgCl>0])))
expect_silent(mc<-getMergeCorrespond(clustMerged,by="original"))
expect_equal(length(mc),length(unique(ogCl[ogCl>0])))
expect_error(getMergeCorrespond(clustMergedAll),"there is no merge clustering in this object")
#check saves even if just plotInfo
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none",plotInfo="all"),"Merging will be done on")
expect_false(is.null(clustMerged@merge_nodeProp))
})
test_that("logFC works",{
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE, reduceMethod="none",
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
#check cluster is same, otherwise won't get same results...
expect_silent(clustWithDendro <- makeDendrogram(cl1,reduceMethod="none"))
#--------
#matrix version
#--------
#only FC
expect_silent(mergedList <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", cutoff=0.1, logFCcutoff=1,calculateAll=FALSE,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedList$nodeProp)))
#calculate All
expect_silent(mergedListAll <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", cutoff=0.1, logFCcutoff=1,calculateAll=TRUE,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedListAll$nodeProp)))
#check calculate all does FC it even if not given as the mergeMethod
# (try both "none" and "Storey")
expect_silent(mergedListAll2 <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="none",
logFCcutoff=1,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedListAll2$nodeProp)))
expect_silent(mergedListAll2 <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey",
logFCcutoff=1,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedListAll2$nodeProp)))
##check giving nodePropTable but need new calculation ("Storey")
expect_silent(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="none",plot=FALSE))
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
##check giving nodePropTable but need new calculation (newFC)
##Also check that actually gives different merging (with logFC10 should)
expect_silent(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList$nodeProp,
dendro=clustWithDendro@dendro_clusters, cutoff=0.1,
mergeMethod="adj", logFCcutoff=10,
plotInfo="none",plot=FALSE))
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
expect_true("adjP_10.0" %in% names(mergedList2$nodeProp))
expect_false(all(mergedList2$nodeProp[,"adjP_10.0"] == mergedList$nodeProp[,"adjP"]))
expect_false(all(mergedList2$nodeMerge[,"isMerged"] == mergedList$nodeMerge[,"isMerged"]))
expect_equal(length(unique(mergedList2$clustering)),3)
expect_equal(length(unique(mergedList$clustering)),5)
##check giving nodePropTable but DON'T need new calculation ("Storey")
expect_message(mergedList3<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedListAll$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="none",plot=FALSE),"Using existing results of per-node significance")
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
##check giving nodePropTable but DON'T need new calculation (logFC)
expect_message(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedListAll$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", logFCcutoff=1,
plotInfo="none",plot=FALSE),"Using existing results of per-node significance")
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
###Test plotting on matrix version:
expect_silent(mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", logFCcutoff=10, plotInfo="adjP_10.0"))
#----------
#on ClusterExperiment
#----------
expect_message(clustMerged <- mergeClusters(clustWithDendro,
mergeMethod="adjP", plotInfo="none", plot=FALSE, DEMethod="limma",
calculateAll=FALSE,cutoff=0.1,logFCcutoff=1),"Merging will be done on")
expect_true(all(c("adjP_1.0") %in% colnames(clustMerged@merge_nodeProp)))
#add to existing with different method
expect_message(clustMerged2 <- mergeClusters(clustMerged, mergeMethod="Storey",
plotInfo="none",cutoff=0.1,plot=FALSE,calculateAll=FALSE),"Merging will be done on")
expect_true(all(c("adjP_1.0") %in% colnames(clustMerged2@merge_nodeProp)))
#rerun previous with different cutoff but same logFC cutoff -- no new calculations needed
expect_message(clustMerged3 <- mergeClusters(clustMerged2,
mergeMethod="adjP", logFCcutoff=1,plotInfo="none",cutoff=0.05,
plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_true(all(c("adjP_1.0") %in% colnames(clustMerged3@merge_nodeProp)))
#redo with different logFC --- pick logFC large enought that changes the proportions to make sure actually merge on right value
expect_message(clustMerged4 <- mergeClusters(clustMerged,
mergeMethod="adjP", logFCcutoff=10,plotInfo="none",cutoff=0.1,plot=FALSE,
calculateAll=FALSE,clusterLabel="merge, logFC"),
"Merging will be done on")
expect_false(all(clustMerged4@merge_nodeProp[,"adjP_10.0"] == clustMerged4@merge_nodeProp[,"adjP"]))
expect_false(all(clustMerged4@merge_nodeMerge[,"isMerged"] == clustMerged@merge_nodeMerge[,"isMerged"]))
expect_equal(length(unique(primaryCluster(clustMerged4))),3)
expect_equal(length(unique(primaryCluster(clustMerged))),5)
##Check labels not getting corrupted when redo
expect_equal(primaryClusterLabel(clustMerged4),"merge, logFC")
expect_message(clustMerged5 <- mergeClusters(clustMerged4,
mergeMethod="adjP", logFCcutoff=10,plotInfo="none",
cutoff=0.1,plot=FALSE,calculateAll=FALSE,
clusterLabel="merge, logFC"),"Merging will be done on")
expect_equal(primaryClusterLabel(clustMerged5),"merge, logFC")
###Test plotting on CE version:
expect_message(clustMerged10 <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plot=TRUE,plotInfo="adjP_10.0",
calculateAll=FALSE,cutoff=0.1,logFCcutoff=10),"Merging will be done on")
expect_silent(plotDendrogram(clustMerged10,mergeInfo="adjP_10.0"))
})
test_that("`mergeClusters` preserves the colData and rowData of SE", {
expect_silent(cl <- clusterSingle(smSimSE,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
expect_silent(clD <- makeDendrogram(cl))
expect_message(cl <- mergeClusters(clD, DEMethod="limma", mergeMethod = "adjP"))
expect_equal(colData(cl),colData(smSimSE))
expect_equal(rownames(cl),rownames(smSimSE))
expect_equal(colnames(cl),colnames(smSimSE))
expect_equal(metadata(cl),metadata(smSimSE))
expect_equal(rowData(cl),rowData(clD))
})
test_that("`mergeClusters` works with unassignedSamples", {
expect_silent(clustWithDendro <- makeDendrogram(ceSim,unassignedSamples = c("outgroup")))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",
plotInfo="mergeMethod",leafType="samples",plotType="colorblock"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",
plotInfo="mergeMethod",leafType="samples",plotType="name"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",
plotInfo="mergeMethod",leafType="clusters",plotType="colorblock"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plotInfo="mergeMethod",leafType="clusters",plotType="name"))
expect_silent(clustWithDendro <- makeDendrogram(ceSim,reduceMethod="mad",unassignedSamples = c("cluster")))
expect_warning(mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="samples",plotType="colorblock"),"You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing")
expect_warning(mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="samples",plotType="name"),"You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing")
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plotInfo="mergeMethod",leafType="clusters",plotType="colorblock",
"You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plotInfo="mergeMethod",leafType="clusters",plotType="name","You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing"))
})
test_that("cluster labels not being internally changed from user input",{
expect_silent(clustWithDendro <- makeDendrogram(ceSim,unassignedSamples = c("outgroup")))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma", mergeMethod="adjP",
plotInfo="mergeMethod",leafType="samples",plotType="colorblock"))
})
Try the clusterExperiment package in your browser
Any scripts or data that you put into this service are public.
clusterExperiment documentation built on Feb. 11, 2021, 2 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context("mergeClusters")
test_that("`mergeClusters` works with matrix",{
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam", clusterArgs=list(k=6)),
isCount=FALSE))
expect_silent(clustWithDendro <- makeDendrogram(cl1))
#matrix version
expect_silent(mergedList <- mergeClusters(x=transformData(cl1), DEMethod="limma", cl=primaryCluster(cl1), dendro=clustWithDendro@dendro_clusters, mergeMethod="adjP", plotInfo="mergeMethod"))
})
test_that("`mergeClusters` works with ClusterExperiment objects", {
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
leg<-clusterLegend(cl1)[[primaryClusterIndex(cl1)]]
leg[,"name"]<-letters[1:6]
clusterLegend(cl1)[[primaryClusterIndex(cl1)]]<-leg
expect_silent(clustWithDendro <- makeDendrogram(cl1))
#check plotting types:
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none",plotInfo="all"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="adjP"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="locfdr"),"Note: Merging will be done on")
expect_warning(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="locfdr",showWarnings=TRUE))
expect_error(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none", plotInfo="mergeMethod"),
"can only plot 'mergeMethod' results if one method is selected")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP",
DEMethod="limma", plotInfo="none"),"Note: Merging will be done on")
#check all methods run
for(method in clusterExperiment:::.availMergeMethods){
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod=method, plotInfo="mergeMethod"),"Note: Merging will be done on")
}
expect_true("mergeClusters" %in% clusterTypes(clustMerged))
expect_true("mergeClusters" %in% colnames(clusterMatrix(clustMerged)))
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma",
plotInfo="mergeMethod",leafType="samples",plotType="colorblock"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="samples",plotType="name"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="clusters",plotType="colorblock"),"Note: Merging will be done on")
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="clusters",plotType="name"),"Note: Merging will be done on")
expect_error(mergeClusters(x=transformData(clustWithDendro), DEMethod="limma",
cl=primaryCluster(clustWithDendro),plot="none",
mergeMethod="adjP",
dendro=clustWithDendro@dendro_samples),
"Not a valid input dendrogram")
expect_error(mergeClusters(clustWithDendro, mergeMethod="adjP"),'argument "DEMethod" is missing, with no default')
#test when merge already exists
expect_message(clustMerged <- mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma"),"Merging will be done on")
expect_silent(primaryClusterIndex(clustMerged)<-2)
expect_silent(clustMerged<- makeDendrogram(clustMerged))
expect_message(clustMerged2<-mergeClusters(clustMerged,mergeMethod="adjP"),"Merging will be done on")
expect_true("mergeClusters.1" %in% clusterTypes(clustMerged2))
expect_true(!"makeConsensus.1" %in% clusterTypes(clustMerged2))
expect_true(!"clusterMany.1" %in% clusterTypes(clustMerged2))
expect_silent(removeClusterings(clustMerged, whichClusters = "mergeClusters"))
})
test_that("`mergeClusters` works with HDF5 assay slot",{
expect_silent(cl1 <- clusterSingle(hdfObj,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
expect_silent(clustWithDendro <- makeDendrogram(cl1))
expect_message(mergedCE <- mergeClusters(x=clustWithDendro,plot=FALSE,
mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod"),
"Merging will be done on")
expect_true(inherits(assay(mergedCE),"DelayedArray"))
})
test_that("saving merge info works",{
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE, reduceMethod="none",
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
#check cluster is same, otherwise won't get same results...
expect_equal(primaryCluster(cl1),c(4,1,1,5,1,2,5,1,1,3,3,3,6,6,4,2,2,2))
#for some reason, clusterSingle not giving reasonable names
expect_silent(clustWithDendro <- makeDendrogram(cl1,reduceMethod="none"))
#Dendrogram:
# --[dendrogram w/ 2 branches and 6 members at h = 1509]
# |--leaf "3"
# `--[dendrogram w/ 2 branches and 5 members at h = 1455]
# |--[dendrogram w/ 2 branches and 2 members at h = 228]
# | |--leaf "1"
# | `--leaf "5"
# `--[dendrogram w/ 2 branches and 3 members at h = 337]
# |--leaf "6"
# `--[dendrogram w/ 2 branches and 2 members at h = 259]
# |--leaf "2"
# `--leaf "4"
#matrix version
expect_silent(mergedList <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", plotInfo="none"))
##check giving nodePropTable
expect_message(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="none"),
"Using existing results of per-node significance")
expect_equal(mergedList2$nodeProp[,"adjP"],mergedList$nodeProp[,"adjP"])
expect_silent(mergedListStorey<-mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="mergeMethod"))
expect_equal(mergedList2$nodeProp[,"Storey"],mergedListStorey$nodeProp[,"Storey"])
expect_message(mergedList2Redo<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList2$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="none", plotInfo=c("all")),"Using existing results of per-node significance")
#------
#on ClusterExperiment
# note need to specify message to see doing it correctly.
#------
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",plotInfo="none",plot=FALSE,calculateAll=FALSE),"Merging will be done on")
expect_equal(clustMerged@merge_dendrocluster_index,clustWithDendro@dendro_index+1)
expect_equal(clustMerged@merge_dendrocluster_index,clustMerged@dendro_index)
expect_equal(clustMerged@merge_index,1)
#add to existing with different method
expect_message(clustMerged2 <- mergeClusters(clustMerged, mergeMethod="Storey",
plotInfo="none",cutoff=0.1,plot=FALSE,calculateAll=FALSE),"Merging will be done on")
expect_equal(clustMerged2@merge_dendrocluster_index,clustMerged@dendro_index+1)
expect_equal(clustMerged2@merge_dendrocluster_index,clustMerged2@dendro_index)
expect_equal(clustMerged2@merge_index,1)
#rerun previous with different cutoff -- no new calculations
expect_message(clustMerged3 <- mergeClusters(clustMerged2,mergeMethod="Storey",
plotInfo="none",cutoff=0.05,plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_equal(clustMerged3@merge_dendrocluster_index,clustMerged2@dendro_index+1)
expect_equal(clustMerged3@merge_dendrocluster_index,clustMerged3@dendro_index)
expect_equal(clustMerged3@merge_index,1)
#do it again with higher value that actually merges -- check correct index updates, etc...
expect_message(clustMerged4 <- mergeClusters(clustMerged3,mergeMethod="Storey",
plotInfo="none",cutoff=0.5,plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_equal(clustMerged4@merge_dendrocluster_index,clustMerged3@dendro_index+1)
expect_equal(clustMerged4@merge_dendrocluster_index,clustMerged4@dendro_index)
expect_equal(clustMerged4@merge_index,1)
expect_equal(clustMerged4@merge_nodeMerge[,"mergeClusterId"],c(NA,NA,1,3,NA))
expect_equal(clustMerged4@merge_nodeMerge[,"isMerged"],c(FALSE,FALSE,TRUE,TRUE,TRUE))
# > clustMerged4@merge_nodeMerge
# Node Contrast isMerged mergeClusterId
# Node1 Node1 X3-(X1+X5+X6+X2+X4)/5 FALSE NA
# Node2 Node2 (X1+X5)/2-(X6+X2+X4)/3 FALSE NA
# Node3 Node3 X1-X5 TRUE 1
# Node4 Node4 X6-(X2+X4)/2 TRUE 3
# Node5 Node5 X2-X4 TRUE NA
# > clustMerged4@merge_nodeProp
# Node Contrast Storey PC adjP locfdr MB JC
# Node1 Node1 X3-(X1+X5+X6+X2+X4)/5 1.0 NA 0.55 NA NA NA
# Node2 Node2 (X1+X5)/2-(X6+X2+X4)/3 1.0 NA 0.75 NA NA NA
# Node3 Node3 X1-X5 0.0 NA 0.10 NA NA NA
# Node4 Node4 X6-(X2+X4)/2 0.1 NA 0.15 NA NA NA
# Node5 Node5 X2-X4 0.4 NA 0.00 NA NA NA
# > clustMerged4@merge_nodeMerge
# NodeId Contrast isMerged mergeClusterId
# InternalNodeId7 InternalNodeId7 X3-(X1+X5+X6+X2+X4)/5 FALSE NA
# InternalNodeId8 InternalNodeId8 (X1+X5)/2-(X6+X2+X4)/3 FALSE NA
# InternalNodeId9 InternalNodeId9 X1-X5 TRUE 1
# InternalNodeId10 InternalNodeId10 X6-(X2+X4)/2 TRUE 3
# InternalNodeId11 InternalNodeId11 X2-X4 TRUE NA
#
#check really gets clusterIds and not names
expect_silent(clusterLegend(clustMerged3)[["clusterSingle"]][,"name"]<-letters[1:6])
expect_message(clustMerged5 <- mergeClusters(clustMerged3, mergeMethod="Storey",
plotInfo="none",cutoff=0.5,plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_equal(clustMerged4@merge_nodeMerge,clustMerged5@merge_nodeMerge)
#helpful for debugging:
# plotDendrogram(clustMerged,show.node=TRUE,show.tip.label=TRUE)
# table(clusterMatrix(clustMerged)[,c(1)],clusterMatrix(clustMerged)[,c(2)])
expect_silent(nodeMergeInfo(clustMerged4))
expect_equal(mergeClusterIndex(clustMerged4),clustMerged4@merge_index)
expect_equal(mergeCutoff(clustMerged4),0.5)
expect_equal(mergeMethod(clustMerged4),"Storey")
#check if can calculate all, but do nothing else
expect_message(clustMergedAll<-mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none",plotInfo="none",cutoff=0.5,plot=FALSE,
calculateAll=TRUE),"Merging will be done on")
expect_false(is.na(clustMergedAll@merge_dendrocluster_index))
expect_true(is.na(clustMergedAll@merge_index))
expect_false(is.null(nodeMergeInfo(clustMergedAll)))
#should erase merge info if call dendrogram
expect_silent(clustMergedErase<-makeDendrogram(clustMerged5))
expect_true(is.na(clustMergedErase@merge_index))
expect_true(is.na(clustMergedErase@merge_dendrocluster_index))
#should erase merge info if call dendrogram
expect_silent(clustMergedErase2<-makeDendrogram(clustMergedAll))
expect_true(is.na(clustMergedErase2@merge_index))
expect_true(is.na(clustMergedErase2@merge_dendrocluster_index))
#test getMergeCorresp
#node clustMerge
mgCl<-clusterMatrix(clustMerged)[,clustMerged@merge_index]
ogCl<-clusterMatrix(clustMerged)[,clustMerged@merge_dendrocluster_index]
expect_silent(mc<-getMergeCorrespond(clustMerged))
expect_equal(length(mc),length(unique(mgCl[mgCl>0])))
expect_silent(mc<-getMergeCorrespond(clustMerged,by="original"))
expect_equal(length(mc),length(unique(ogCl[ogCl>0])))
expect_error(getMergeCorrespond(clustMergedAll),"there is no merge clustering in this object")
#check saves even if just plotInfo
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="none",plotInfo="all"),"Merging will be done on")
expect_false(is.null(clustMerged@merge_nodeProp))
})
test_that("logFC works",{
expect_silent(cl1 <- clusterSingle(smSimData,
subsample=FALSE, sequential=FALSE, reduceMethod="none",
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
#check cluster is same, otherwise won't get same results...
expect_silent(clustWithDendro <- makeDendrogram(cl1,reduceMethod="none"))
#--------
#matrix version
#--------
#only FC
expect_silent(mergedList <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", cutoff=0.1, logFCcutoff=1,calculateAll=FALSE,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedList$nodeProp)))
#calculate All
expect_silent(mergedListAll <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", cutoff=0.1, logFCcutoff=1,calculateAll=TRUE,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedListAll$nodeProp)))
#check calculate all does FC it even if not given as the mergeMethod
# (try both "none" and "Storey")
expect_silent(mergedListAll2 <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="none",
logFCcutoff=1,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedListAll2$nodeProp)))
expect_silent(mergedListAll2 <- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey",
logFCcutoff=1,plotInfo="none",plot=FALSE))
expect_true(all(c(clusterExperiment:::.availMergeMethods,"adjP_1.0") %in% colnames(mergedListAll2$nodeProp)))
##check giving nodePropTable but need new calculation ("Storey")
expect_silent(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="none",plot=FALSE))
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
##check giving nodePropTable but need new calculation (newFC)
##Also check that actually gives different merging (with logFC10 should)
expect_silent(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedList$nodeProp,
dendro=clustWithDendro@dendro_clusters, cutoff=0.1,
mergeMethod="adj", logFCcutoff=10,
plotInfo="none",plot=FALSE))
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
expect_true("adjP_10.0" %in% names(mergedList2$nodeProp))
expect_false(all(mergedList2$nodeProp[,"adjP_10.0"] == mergedList$nodeProp[,"adjP"]))
expect_false(all(mergedList2$nodeMerge[,"isMerged"] == mergedList$nodeMerge[,"isMerged"]))
expect_equal(length(unique(mergedList2$clustering)),3)
expect_equal(length(unique(mergedList$clustering)),5)
##check giving nodePropTable but DON'T need new calculation ("Storey")
expect_message(mergedList3<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedListAll$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="Storey", plotInfo="none",plot=FALSE),"Using existing results of per-node significance")
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
##check giving nodePropTable but DON'T need new calculation (logFC)
expect_message(mergedList2<- mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1), nodePropTable=mergedListAll$nodeProp,
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", logFCcutoff=1,
plotInfo="none",plot=FALSE),"Using existing results of per-node significance")
expect_equal(mergedList2$nodeProp[,"adjP_1.0"],mergedList$nodeProp[,"adjP_1.0"])
###Test plotting on matrix version:
expect_silent(mergeClusters(x=transformData(cl1), DEMethod="limma",
cl=primaryCluster(cl1),
dendro=clustWithDendro@dendro_clusters,
mergeMethod="adjP", logFCcutoff=10, plotInfo="adjP_10.0"))
#----------
#on ClusterExperiment
#----------
expect_message(clustMerged <- mergeClusters(clustWithDendro,
mergeMethod="adjP", plotInfo="none", plot=FALSE, DEMethod="limma",
calculateAll=FALSE,cutoff=0.1,logFCcutoff=1),"Merging will be done on")
expect_true(all(c("adjP_1.0") %in% colnames(clustMerged@merge_nodeProp)))
#add to existing with different method
expect_message(clustMerged2 <- mergeClusters(clustMerged, mergeMethod="Storey",
plotInfo="none",cutoff=0.1,plot=FALSE,calculateAll=FALSE),"Merging will be done on")
expect_true(all(c("adjP_1.0") %in% colnames(clustMerged2@merge_nodeProp)))
#rerun previous with different cutoff but same logFC cutoff -- no new calculations needed
expect_message(clustMerged3 <- mergeClusters(clustMerged2,
mergeMethod="adjP", logFCcutoff=1,plotInfo="none",cutoff=0.05,
plot=FALSE,calculateAll=FALSE),"Using existing results of per-node significance")
expect_true(all(c("adjP_1.0") %in% colnames(clustMerged3@merge_nodeProp)))
#redo with different logFC --- pick logFC large enought that changes the proportions to make sure actually merge on right value
expect_message(clustMerged4 <- mergeClusters(clustMerged,
mergeMethod="adjP", logFCcutoff=10,plotInfo="none",cutoff=0.1,plot=FALSE,
calculateAll=FALSE,clusterLabel="merge, logFC"),
"Merging will be done on")
expect_false(all(clustMerged4@merge_nodeProp[,"adjP_10.0"] == clustMerged4@merge_nodeProp[,"adjP"]))
expect_false(all(clustMerged4@merge_nodeMerge[,"isMerged"] == clustMerged@merge_nodeMerge[,"isMerged"]))
expect_equal(length(unique(primaryCluster(clustMerged4))),3)
expect_equal(length(unique(primaryCluster(clustMerged))),5)
##Check labels not getting corrupted when redo
expect_equal(primaryClusterLabel(clustMerged4),"merge, logFC")
expect_message(clustMerged5 <- mergeClusters(clustMerged4,
mergeMethod="adjP", logFCcutoff=10,plotInfo="none",
cutoff=0.1,plot=FALSE,calculateAll=FALSE,
clusterLabel="merge, logFC"),"Merging will be done on")
expect_equal(primaryClusterLabel(clustMerged5),"merge, logFC")
###Test plotting on CE version:
expect_message(clustMerged10 <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plot=TRUE,plotInfo="adjP_10.0",
calculateAll=FALSE,cutoff=0.1,logFCcutoff=10),"Merging will be done on")
expect_silent(plotDendrogram(clustMerged10,mergeInfo="adjP_10.0"))
})
test_that("`mergeClusters` preserves the colData and rowData of SE", {
expect_silent(cl <- clusterSingle(smSimSE,
subsample=FALSE, sequential=FALSE,
mainClusterArgs=list(clusterFunction="pam",clusterArgs=list(k=6)),
isCount=FALSE))
expect_silent(clD <- makeDendrogram(cl))
expect_message(cl <- mergeClusters(clD, DEMethod="limma", mergeMethod = "adjP"))
expect_equal(colData(cl),colData(smSimSE))
expect_equal(rownames(cl),rownames(smSimSE))
expect_equal(colnames(cl),colnames(smSimSE))
expect_equal(metadata(cl),metadata(smSimSE))
expect_equal(rowData(cl),rowData(clD))
})
test_that("`mergeClusters` works with unassignedSamples", {
expect_silent(clustWithDendro <- makeDendrogram(ceSim,unassignedSamples = c("outgroup")))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",
plotInfo="mergeMethod",leafType="samples",plotType="colorblock"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",
plotInfo="mergeMethod",leafType="samples",plotType="name"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP",
plotInfo="mergeMethod",leafType="clusters",plotType="colorblock"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plotInfo="mergeMethod",leafType="clusters",plotType="name"))
expect_silent(clustWithDendro <- makeDendrogram(ceSim,reduceMethod="mad",unassignedSamples = c("cluster")))
expect_warning(mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="samples",plotType="colorblock"),"You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing")
expect_warning(mergeClusters(clustWithDendro, mergeMethod="adjP", DEMethod="limma", plotInfo="mergeMethod",leafType="samples",plotType="name"),"You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing")
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plotInfo="mergeMethod",leafType="clusters",plotType="colorblock",
"You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing"))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma",
mergeMethod="adjP", plotInfo="mergeMethod",leafType="clusters",plotType="name","You cannot set 'leafType' to 'samples' in plotting mergeClusters unless the dendrogram was made with unassigned/missing"))
})
test_that("cluster labels not being internally changed from user input",{
expect_silent(clustWithDendro <- makeDendrogram(ceSim,unassignedSamples = c("outgroup")))
expect_message(clustMerged <- mergeClusters(clustWithDendro, DEMethod="limma", mergeMethod="adjP",
plotInfo="mergeMethod",leafType="samples",plotType="colorblock"))
})
Try the clusterExperiment package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.