tests/testthat/test-heatmaps.R
In epurdom/clusterCells: Compare Clusterings for Single-Cell Sequencing
##put separate so that not too long without output...
context("Heatmap functions")
plotAll<-FALSE #set to true to actually SEE the plots; otherwise for TravisCI, where no visual, runs quicker with FALSE
###Note some are still run with plot=TRUE to check that works with aheatmap. Only a fraction not plotted.
test_that("`setBreaks`", {
setBreaks(smSimData)
setBreaks(smSimData,breaks=0.99)
x<-setBreaks(smSimData,breaks=0.99,makeSymmetric=TRUE)
expect_equal(max(x),-min(x))
expect_equal(x,setBreaks(smSimData,breaks=0.01,makeSymmetric=TRUE))
expect_warning(y<-setBreaks(smSimData,breaks=10))
expect_equal(length(y),10)
})
test_that("`plotHeatmap` works with matrix objects", {
# these require that they actually be plotted...
expect_silent(x1<-plotHeatmap(data=smSimData))
a1<-NMF::aheatmap(smSimData)
expect_equal(x1$aheatmapOut,a1)
expect_silent(x2<-plotHeatmap(data=smSimCount,
clusterSamplesData=smSimData,
clusterFeaturesData=smSimData))
#for some reason, labels on dendrogram move from character to numeric so can't test entire object...
expect_equal(x1$aheatmapOut$rowInd,x2$aheatmapOut$rowInd)
expect_equal(x1$aheatmapOut$colInd,x2$aheatmapOut$colInd)
#check internal alignment of colData (alignColData=TRUE) is working:
colData<-clusterMatrix(smSimCE)
expect_silent(alList<-plotClusters(colData))
alCol<-clusterExperiment:::.convertToAheatmap(alList$clusterLegend, names=FALSE)
#these should be same plots:
expect_silent(x1<-plotHeatmap(data=smSimData[,alList$orderSamples],
colData=colData[alList$orderSamples,1:10],
clusterLegend=alCol,clusterSamples=FALSE,
clusterFeatures=FALSE,plot=plotAll))
expect_silent(x2<-plotHeatmap(data=smSimData[,alList$orderSamples],
colData=colData[alList$orderSamples,1:10],
alignColData=TRUE,clusterFeatures=FALSE,
clusterSamples=FALSE,plot=plotAll))
# Should get this working so proper test, but more a problem because in different order, otherwise the same. Don't want to deal with this right now.
# expect_equal(lapply(x1$clusterLegend,function(x){x[,c("clusterIds","color")]}),lapply(x2$clusterLegend,function(x){x[,c("clusterIds","color")]}))
expect_error( plotHeatmap(data=smSimData,Rowv=TRUE, plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,Colv=TRUE, plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,
colorScale=seqPal5,color=TRUE, plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,
annCol=rnorm(n=ncol(smSimData)), plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,
annColors=list(a=c("blue","green")), plot=plotAll),
"arguments to aheatmap cannot be set by the user")
##Should add tests that pass aheatmap arguments correctly.
})
test_that("`plotHeatmap` works with hdf5 objects", {
# These are slow!
skip_on_os("windows")
skip_on_os("mac")
expect_silent(plotHeatmap(hdfObj))
})
test_that("`plotHeatmap` works with ClusterExperiment and SummarizedExperiment objects", {
expect_silent(plotHeatmap(cc))
expect_silent(plotHeatmap(cc,whichClusters="none", plot=plotAll))
expect_warning(plotHeatmap(cc,whichClusters="workflow", plot=plotAll) ,
"whichClusters value does not match any clusters") #there are no workflow for this one
expect_warning(plotHeatmap(smSimCE,whichClusters="workflow", plot=plotAll,
overRideClusterLimit=TRUE),
"More than 10 annotations/clusterings can result in incomprehensible errors in aheamap")
expect_warning(plotHeatmap(smSimCE,whichClusters=15:20, plot=plotAll),
"given whichClusters value does not match any clusters")
expect_error( plotHeatmap(smSimCE,whichClusters="all", plot=plotAll,
alignColData=TRUE, overRideClusterLimit=FALSE),
"More than 10 annotations/clusterings")
expect_warning(plotHeatmap(smSimCE, plot=plotAll,
whichClusters="all",
alignColData=FALSE,overRideClusterLimit=TRUE))
#test colData
expect_error(plotHeatmap(cc,colData="A", plot=plotAll), "no colData for object data")
expect_silent(plotHeatmap(smSimCE,colData="all", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,colData="A",plot=plotAll))
expect_silent(plotHeatmap(smSimCE,colData=2:3,plot=plotAll))
#check that it pulls the names, not the clusterIds.
expect_silent(clusterLegend(cc)[[1]][,"name"]<-letters[1:nrow(clusterLegend(cc)[[1]])])
expect_silent(plotHeatmap(cc, plot=plotAll))
#check user setting clusterLegend
x<-palette()[1:7]
names(x)<-clusterLegend(cc)$Cluster1[,"name"]
expect_silent(plotHeatmap(cc,
clusterLegend=list("Cluster1"=x),plot=plotAll))
expect_silent(plotHeatmap(cc, plot=plotAll,
clusterLegend=list("Cluster1"=palette()[1:7])))
expect_silent(plotHeatmap(smSimCE,
colData="A",clusterLegend=list("A"=palette()[1:4]),
plot=plotAll))
########################
########################
# the following checks work outside of the test but inside test_that, they hit errors
# possibly issue with testthat? Not evaluating for now.
########################
########################
#
# plotHeatmap(smSimCE, colData="all", whichClusters="none")
#
# #this test doesn't work -- for some reason, expect_warning environment hits error that don't see at the consule.
# plotHeatmap(smSimCE,whichClusters="all",alignColData=TRUE,overRideClusterLimit=TRUE)
# expect_warning( plotHeatmap(smSimCE, whichClusters="all", alignColData=TRUE, overRideClusterLimit=TRUE)
# , "More than 10 annotations/clusterings")
#
# # create some names to see if keeps names with alignColData=TRUE
# # only can check manually, not with testthat.
# # BUG!: doesn't work. looses their -1/-2 designation... haven't fixed yet.
# clLeg<-clusterLegend(smSimCE)
# clLeg[[1]][,"name"]<-LETTERS[1:nrow(clLeg[[1]])]
# clusterLegend(smSimCE)<-clLeg
# plotHeatmap(smSimCE, whichClusters="all", alignColData=TRUE,overRideClusterLimit=TRUE)
#
})
test_that("`plotHeatmap` visualization choices/feature choices all work", {
expect_silent(plotHeatmap(smSimCE,
visualizeData=smSimCount,plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="original",plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="centeredAndScaled",plot=plotAll))
# even if visualizeData="orginal, still clsuter on transformed. Should make unit test out of below that get same:
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed", clusterSamplesData="hclust",
plot=plotAll))
orderSamples(smSimCE)<-sample(1:nSamples(smSimCE))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",
clusterSamplesData="orderSamplesValue", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",
clusterSamplesData="primaryCluster", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",
clusterSamplesData=c(3,4,5), plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData="all", plot=plotAll))
###The following subset the genes
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData="var", nFeatures=3, plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData=3:5, nFeatures=3, plot=plotAll))
## expect error because no row names in smSimCE
expect_error(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData=paste("Gene",3:5), nFeatures=3),
"Cannot give feature names in clusterFeaturesData unless")
##set rownames and should work
smSimCE2<-smSimCE
row.names(smSimCE2)<-paste("Gene",1:NROW(smSimCE))
expect_silent(plotHeatmap(smSimCE2, plot=plotAll,
visualizeData="transform",
clusterFeaturesData=paste("Gene",3:5), nFeatures=3))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData="PCA", nFeatures=10,
clusterSamplesData="hclust", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterSamplesData="dendrogramValue", plot=plotAll))
#test works with outside dataset
expect_silent(plotHeatmap(smSimCE,
visualizeData=assay(smSimCE)[1:10,],plot=plotAll))
expect_error(plotHeatmap(smSimCE,
visualizeData=assay(smSimCE)[,1:5]))
})
test_that("`makeBlankData` works", {
##call directly, features
gps<-list(c(3,6,7),c(2,1))
expect_silent(xx<-makeBlankData(assay(smSimCE),
groupsOfFeatures=gps))
expect_equal(nrow(xx$dataWBlanks),length(xx$rowNamesWBlanks))
whBlankNames<-which(xx$rowNamesWBlanks=="")
expect_equal(xx$rowNamesWBlanks[-whBlankNames],
as.character(unlist(gps)) )
whBlankRows<-as.numeric(which(apply(xx$dataWBlanks,1,
function(x){all(is.na(x))})))
expect_equal(whBlankRows,whBlankNames)
expect_equal(whBlankRows,4)
##call directly, samples
gps<-list(c(3,6,7),c(2,1))
expect_silent(xy<-makeBlankData(assay(smSimCE),groupsOfSamples=gps))
expect_equal(ncol(xy$dataWBlanks),length(xy$colNamesWBlanks))
whBlankNames<-which(xy$colNamesWBlanks=="")
expect_equal(xy$colNamesWBlanks[-whBlankNames],
as.character(unlist(gps)) )
whBlankCols<-as.numeric(which(apply(xy$dataWBlanks,2,
function(x){all(is.na(x))})))
expect_equal(whBlankCols,whBlankNames)
expect_equal(whBlankCols,4)
##call directly, features and samples
gpsR<-list(c(3,6,7),c(2,1))
gpsC<-list(c(8,1,3),c(9,10))
expect_silent(yy<-makeBlankData(assay(smSimCE),
groupsOfFeatures=gpsR,groupsOfSamples=gpsC))
expect_equal(ncol(yy$dataWBlanks),length(yy$colNamesWBlanks))
expect_equal(nrow(yy$dataWBlanks),length(yy$rowNamesWBlanks))
whBlankNames<-which(yy$colNamesWBlanks=="")
expect_equal(yy$colNamesWBlanks[-whBlankNames],
as.character(unlist(gpsC)) )
whBlankCols<-as.numeric(which(apply(yy$dataWBlanks,2,
function(x){all(is.na(x))})))
expect_equal(whBlankCols,whBlankNames)
expect_equal(whBlankCols,4)
whBlankNames<-which(yy$rowNamesWBlanks=="")
expect_equal(yy$rowNamesWBlanks[-whBlankNames],
as.character(unlist(gpsR)) )
whBlankRows<-as.numeric(which(apply(yy$dataWBlanks,1,
function(x){all(is.na(x))})))
expect_equal(whBlankRows,whBlankNames)
expect_equal(whBlankRows,4)
##call within plotHeatmap (serves as test of NA capabilities)
expect_silent(plotHeatmap(smSimCE,clusterFeaturesData=gps))
expect_warning(plotHeatmap(smSimCE,clusterFeaturesData=gps,breaks=40))
expect_silent(plotHeatmap(smSimCE,clusterFeaturesData=gps,breaks=.99))
})
test_that("`plotCoClustering` works", {
expect_error(plotCoClustering(smSimCE),"coClustering slot is empty")
#following gives all -1, but creates coClustering
expect_silent(smMin1<-
makeConsensus(smSimCE,whichClusters=10:13,proportion=.99))
# smMin1<-makeConsensus(smSimCE,whichClusters=1:8,proportion=.95) #use to give all -1, but creates coClustering but something changed -- couldn't figure it out!!!
expect_silent(plotCoClustering(smMin1,clusterSamplesData="hclust"))
## Have changed so now changes it internally to primary cluster then hclust
expect_warning( plotCoClustering(smMin1,
clusterSamplesData="dendrogramValue", plot=plotAll),
"cannot make dendrogram from 'data'")
expect_silent(sm<-makeConsensus(smSimCE,whichClusters=1:4,proportion=.5))
expect_silent(plotCoClustering(sm,clusterSamplesData="dendrogramValue"))
# ## Test on object that has a merge done on it
# ## FIXME:
# ## This has surprising error and warning due to phylo conversion
# ## -- need to go back to it
# ## (also error on release version!)
# expect_silent(clustNothing <- clusterMany(mat,
# ks=c(3,4),clusterFunction="pam",
# subsample=FALSE, sequential=FALSE,
# isCount=FALSE,verbose=FALSE))
# expect_silent(clustNothing<-makeConsensus(clustNothing,
# proportion=1,minSize=1,whichClusters = "clusterMany"))
# expect_silent(clustNothing <- makeDendrogram(clustNothing))
# expect_message(clustNothing<- mergeClusters(clustNothing,
# DEMethod="limma",
# mergeMethod="adjP",plotInfo="none"),
# "Note: Merging will be done on")
# expect_silent(plotCoClustering(clustNothing))
})
epurdom/clusterCells documentation built on April 28, 2024, 8:14 p.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.
##put separate so that not too long without output...
context("Heatmap functions")
plotAll<-FALSE #set to true to actually SEE the plots; otherwise for TravisCI, where no visual, runs quicker with FALSE
###Note some are still run with plot=TRUE to check that works with aheatmap. Only a fraction not plotted.
test_that("`setBreaks`", {
setBreaks(smSimData)
setBreaks(smSimData,breaks=0.99)
x<-setBreaks(smSimData,breaks=0.99,makeSymmetric=TRUE)
expect_equal(max(x),-min(x))
expect_equal(x,setBreaks(smSimData,breaks=0.01,makeSymmetric=TRUE))
expect_warning(y<-setBreaks(smSimData,breaks=10))
expect_equal(length(y),10)
})
test_that("`plotHeatmap` works with matrix objects", {
# these require that they actually be plotted...
expect_silent(x1<-plotHeatmap(data=smSimData))
a1<-NMF::aheatmap(smSimData)
expect_equal(x1$aheatmapOut,a1)
expect_silent(x2<-plotHeatmap(data=smSimCount,
clusterSamplesData=smSimData,
clusterFeaturesData=smSimData))
#for some reason, labels on dendrogram move from character to numeric so can't test entire object...
expect_equal(x1$aheatmapOut$rowInd,x2$aheatmapOut$rowInd)
expect_equal(x1$aheatmapOut$colInd,x2$aheatmapOut$colInd)
#check internal alignment of colData (alignColData=TRUE) is working:
colData<-clusterMatrix(smSimCE)
expect_silent(alList<-plotClusters(colData))
alCol<-clusterExperiment:::.convertToAheatmap(alList$clusterLegend, names=FALSE)
#these should be same plots:
expect_silent(x1<-plotHeatmap(data=smSimData[,alList$orderSamples],
colData=colData[alList$orderSamples,1:10],
clusterLegend=alCol,clusterSamples=FALSE,
clusterFeatures=FALSE,plot=plotAll))
expect_silent(x2<-plotHeatmap(data=smSimData[,alList$orderSamples],
colData=colData[alList$orderSamples,1:10],
alignColData=TRUE,clusterFeatures=FALSE,
clusterSamples=FALSE,plot=plotAll))
# Should get this working so proper test, but more a problem because in different order, otherwise the same. Don't want to deal with this right now.
# expect_equal(lapply(x1$clusterLegend,function(x){x[,c("clusterIds","color")]}),lapply(x2$clusterLegend,function(x){x[,c("clusterIds","color")]}))
expect_error( plotHeatmap(data=smSimData,Rowv=TRUE, plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,Colv=TRUE, plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,
colorScale=seqPal5,color=TRUE, plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,
annCol=rnorm(n=ncol(smSimData)), plot=plotAll),
"arguments to aheatmap cannot be set by the user")
expect_error( plotHeatmap(data=smSimData,
annColors=list(a=c("blue","green")), plot=plotAll),
"arguments to aheatmap cannot be set by the user")
##Should add tests that pass aheatmap arguments correctly.
})
test_that("`plotHeatmap` works with hdf5 objects", {
# These are slow!
skip_on_os("windows")
skip_on_os("mac")
expect_silent(plotHeatmap(hdfObj))
})
test_that("`plotHeatmap` works with ClusterExperiment and SummarizedExperiment objects", {
expect_silent(plotHeatmap(cc))
expect_silent(plotHeatmap(cc,whichClusters="none", plot=plotAll))
expect_warning(plotHeatmap(cc,whichClusters="workflow", plot=plotAll) ,
"whichClusters value does not match any clusters") #there are no workflow for this one
expect_warning(plotHeatmap(smSimCE,whichClusters="workflow", plot=plotAll,
overRideClusterLimit=TRUE),
"More than 10 annotations/clusterings can result in incomprehensible errors in aheamap")
expect_warning(plotHeatmap(smSimCE,whichClusters=15:20, plot=plotAll),
"given whichClusters value does not match any clusters")
expect_error( plotHeatmap(smSimCE,whichClusters="all", plot=plotAll,
alignColData=TRUE, overRideClusterLimit=FALSE),
"More than 10 annotations/clusterings")
expect_warning(plotHeatmap(smSimCE, plot=plotAll,
whichClusters="all",
alignColData=FALSE,overRideClusterLimit=TRUE))
#test colData
expect_error(plotHeatmap(cc,colData="A", plot=plotAll), "no colData for object data")
expect_silent(plotHeatmap(smSimCE,colData="all", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,colData="A",plot=plotAll))
expect_silent(plotHeatmap(smSimCE,colData=2:3,plot=plotAll))
#check that it pulls the names, not the clusterIds.
expect_silent(clusterLegend(cc)[[1]][,"name"]<-letters[1:nrow(clusterLegend(cc)[[1]])])
expect_silent(plotHeatmap(cc, plot=plotAll))
#check user setting clusterLegend
x<-palette()[1:7]
names(x)<-clusterLegend(cc)$Cluster1[,"name"]
expect_silent(plotHeatmap(cc,
clusterLegend=list("Cluster1"=x),plot=plotAll))
expect_silent(plotHeatmap(cc, plot=plotAll,
clusterLegend=list("Cluster1"=palette()[1:7])))
expect_silent(plotHeatmap(smSimCE,
colData="A",clusterLegend=list("A"=palette()[1:4]),
plot=plotAll))
########################
########################
# the following checks work outside of the test but inside test_that, they hit errors
# possibly issue with testthat? Not evaluating for now.
########################
########################
#
# plotHeatmap(smSimCE, colData="all", whichClusters="none")
#
# #this test doesn't work -- for some reason, expect_warning environment hits error that don't see at the consule.
# plotHeatmap(smSimCE,whichClusters="all",alignColData=TRUE,overRideClusterLimit=TRUE)
# expect_warning( plotHeatmap(smSimCE, whichClusters="all", alignColData=TRUE, overRideClusterLimit=TRUE)
# , "More than 10 annotations/clusterings")
#
# # create some names to see if keeps names with alignColData=TRUE
# # only can check manually, not with testthat.
# # BUG!: doesn't work. looses their -1/-2 designation... haven't fixed yet.
# clLeg<-clusterLegend(smSimCE)
# clLeg[[1]][,"name"]<-LETTERS[1:nrow(clLeg[[1]])]
# clusterLegend(smSimCE)<-clLeg
# plotHeatmap(smSimCE, whichClusters="all", alignColData=TRUE,overRideClusterLimit=TRUE)
#
})
test_that("`plotHeatmap` visualization choices/feature choices all work", {
expect_silent(plotHeatmap(smSimCE,
visualizeData=smSimCount,plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="original",plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="centeredAndScaled",plot=plotAll))
# even if visualizeData="orginal, still clsuter on transformed. Should make unit test out of below that get same:
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed", clusterSamplesData="hclust",
plot=plotAll))
orderSamples(smSimCE)<-sample(1:nSamples(smSimCE))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",
clusterSamplesData="orderSamplesValue", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",
clusterSamplesData="primaryCluster", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transformed",
clusterSamplesData=c(3,4,5), plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData="all", plot=plotAll))
###The following subset the genes
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData="var", nFeatures=3, plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData=3:5, nFeatures=3, plot=plotAll))
## expect error because no row names in smSimCE
expect_error(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData=paste("Gene",3:5), nFeatures=3),
"Cannot give feature names in clusterFeaturesData unless")
##set rownames and should work
smSimCE2<-smSimCE
row.names(smSimCE2)<-paste("Gene",1:NROW(smSimCE))
expect_silent(plotHeatmap(smSimCE2, plot=plotAll,
visualizeData="transform",
clusterFeaturesData=paste("Gene",3:5), nFeatures=3))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterFeaturesData="PCA", nFeatures=10,
clusterSamplesData="hclust", plot=plotAll))
expect_silent(plotHeatmap(smSimCE,
visualizeData="transform",
clusterSamplesData="dendrogramValue", plot=plotAll))
#test works with outside dataset
expect_silent(plotHeatmap(smSimCE,
visualizeData=assay(smSimCE)[1:10,],plot=plotAll))
expect_error(plotHeatmap(smSimCE,
visualizeData=assay(smSimCE)[,1:5]))
})
test_that("`makeBlankData` works", {
##call directly, features
gps<-list(c(3,6,7),c(2,1))
expect_silent(xx<-makeBlankData(assay(smSimCE),
groupsOfFeatures=gps))
expect_equal(nrow(xx$dataWBlanks),length(xx$rowNamesWBlanks))
whBlankNames<-which(xx$rowNamesWBlanks=="")
expect_equal(xx$rowNamesWBlanks[-whBlankNames],
as.character(unlist(gps)) )
whBlankRows<-as.numeric(which(apply(xx$dataWBlanks,1,
function(x){all(is.na(x))})))
expect_equal(whBlankRows,whBlankNames)
expect_equal(whBlankRows,4)
##call directly, samples
gps<-list(c(3,6,7),c(2,1))
expect_silent(xy<-makeBlankData(assay(smSimCE),groupsOfSamples=gps))
expect_equal(ncol(xy$dataWBlanks),length(xy$colNamesWBlanks))
whBlankNames<-which(xy$colNamesWBlanks=="")
expect_equal(xy$colNamesWBlanks[-whBlankNames],
as.character(unlist(gps)) )
whBlankCols<-as.numeric(which(apply(xy$dataWBlanks,2,
function(x){all(is.na(x))})))
expect_equal(whBlankCols,whBlankNames)
expect_equal(whBlankCols,4)
##call directly, features and samples
gpsR<-list(c(3,6,7),c(2,1))
gpsC<-list(c(8,1,3),c(9,10))
expect_silent(yy<-makeBlankData(assay(smSimCE),
groupsOfFeatures=gpsR,groupsOfSamples=gpsC))
expect_equal(ncol(yy$dataWBlanks),length(yy$colNamesWBlanks))
expect_equal(nrow(yy$dataWBlanks),length(yy$rowNamesWBlanks))
whBlankNames<-which(yy$colNamesWBlanks=="")
expect_equal(yy$colNamesWBlanks[-whBlankNames],
as.character(unlist(gpsC)) )
whBlankCols<-as.numeric(which(apply(yy$dataWBlanks,2,
function(x){all(is.na(x))})))
expect_equal(whBlankCols,whBlankNames)
expect_equal(whBlankCols,4)
whBlankNames<-which(yy$rowNamesWBlanks=="")
expect_equal(yy$rowNamesWBlanks[-whBlankNames],
as.character(unlist(gpsR)) )
whBlankRows<-as.numeric(which(apply(yy$dataWBlanks,1,
function(x){all(is.na(x))})))
expect_equal(whBlankRows,whBlankNames)
expect_equal(whBlankRows,4)
##call within plotHeatmap (serves as test of NA capabilities)
expect_silent(plotHeatmap(smSimCE,clusterFeaturesData=gps))
expect_warning(plotHeatmap(smSimCE,clusterFeaturesData=gps,breaks=40))
expect_silent(plotHeatmap(smSimCE,clusterFeaturesData=gps,breaks=.99))
})
test_that("`plotCoClustering` works", {
expect_error(plotCoClustering(smSimCE),"coClustering slot is empty")
#following gives all -1, but creates coClustering
expect_silent(smMin1<-
makeConsensus(smSimCE,whichClusters=10:13,proportion=.99))
# smMin1<-makeConsensus(smSimCE,whichClusters=1:8,proportion=.95) #use to give all -1, but creates coClustering but something changed -- couldn't figure it out!!!
expect_silent(plotCoClustering(smMin1,clusterSamplesData="hclust"))
## Have changed so now changes it internally to primary cluster then hclust
expect_warning( plotCoClustering(smMin1,
clusterSamplesData="dendrogramValue", plot=plotAll),
"cannot make dendrogram from 'data'")
expect_silent(sm<-makeConsensus(smSimCE,whichClusters=1:4,proportion=.5))
expect_silent(plotCoClustering(sm,clusterSamplesData="dendrogramValue"))
# ## Test on object that has a merge done on it
# ## FIXME:
# ## This has surprising error and warning due to phylo conversion
# ## -- need to go back to it
# ## (also error on release version!)
# expect_silent(clustNothing <- clusterMany(mat,
# ks=c(3,4),clusterFunction="pam",
# subsample=FALSE, sequential=FALSE,
# isCount=FALSE,verbose=FALSE))
# expect_silent(clustNothing<-makeConsensus(clustNothing,
# proportion=1,minSize=1,whichClusters = "clusterMany"))
# expect_silent(clustNothing <- makeDendrogram(clustNothing))
# expect_message(clustNothing<- mergeClusters(clustNothing,
# DEMethod="limma",
# mergeMethod="adjP",plotInfo="none"),
# "Note: Merging will be done on")
# expect_silent(plotCoClustering(clustNothing))
})
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.