tests/testthat/setup_create_objects.R

In epurdom/clusterExperiment: Compare Clusterings for Single-Cell Sequencing

##Code for timing the results of the tests:
# testOutput<-testOutput<-test_dir("testthat/",reporter=ListReporter)
# timingDf<-do.call("rbind", lapply(testOutput, function(x){data.frame(file=x$file, test=x$test, time=round(x$real,2))}))
# timingDf<-timingDf[order(timingDf$time),]
# write.table(file="testTimings.txt", x=timingDf)

###Note: any changes to this file should be at the END so as to not mess up the seed calls.
library(clusterExperiment)
# library(devtools)
# load_all()
data(simData, envir = environment())
if(ncol(simData) != 300) {
  stop("not current version of simData")
  #get all kinds of annoyances because using old version.
  #Can delete this once package is stabilized.
}
## make sure the tests are reproducible
## This code uses old version of sampling to match what was used. Will give warning. 
suppressWarnings(RNGversion("3.5.0"))
set.seed(23)

#################################
###Simple, trivial sized objects for testing:
# mat=20x15 matrix of data with row and column names
# labMat 15 x 2 matrix of numberic clusters, labeled 2-5, plus -1,-2 values with column names
# sData 15 x 3 matrix of data on the samples, a factor, continuous, and character variable with column names
# gData 20 x 4 matrix of data on the features: factor, continuous, character (like sData) with column names
# mData list of length 2 of random information to be metaData
# se a Summarized experiment with rowData, colData, and metaData slots
#################################
mat <- matrix(data=rnorm(20*15), ncol=15)
mat[1,1]<- -1 #force a negative value
colnames(mat)<-paste("Sample",1:ncol(mat))
rownames(mat)<-paste("Gene",1:nrow(mat))
dissMat<-as.matrix(dist(t(mat)))
numLabels <- as.character(gl(5, 3))
numLabels[c(1:2)]<- c("-1","-2") #make sure some not assigned
numLabels<-factor(numLabels)
chLabels<-rep(LETTERS[1:5],each=3)
chLabels[c(2:3)]<- c("-1","-2") #make sure some not assigned
labMat<-cbind(as.numeric(as.character(numLabels)),as.numeric(as.character(numLabels)))
colnames(labMat)<-c("Cluster1","Cluster2")
sData<-data.frame(sample(letters[2:5],size=NCOL(mat),replace=TRUE),sample(2:5,size=NCOL(mat),replace=TRUE))
sData<-data.frame(sData,sample(LETTERS[2:5],size=NCOL(mat),replace=TRUE),stringsAsFactors=FALSE)
gData<-data.frame(sample(letters[2:5],size=NROW(mat),replace=TRUE),sample(2:5,size=NROW(mat),replace=TRUE))
gData<-data.frame(gData,sample(LETTERS[2:5],size=NROW(mat),replace=TRUE),stringsAsFactors=FALSE)
colnames(sData)<-c("A","B","C")
colnames(gData)<-c("a","b","c")
mData<-list(first=c(1,2,3),second=c("Information"))
se <- SummarizedExperiment(mat,colData=sData,rowData=gData,metadata=mData)
cc <- ClusterExperiment(mat, labMat, transformation = function(x){x})
ccSE<-ClusterExperiment(se, labMat, transformation=function(x){x})


#################################
###Larger sized objects based on simData/simCount:
#################################
data(simData)
if(ncol(simData)!=300) stop("not current version of simData") #get all kinds of annoyances because using old version.
simSData<-data.frame(sample(letters[2:5],size=NCOL(simData),replace=TRUE),sample(2:5,size=NCOL(simData),replace=TRUE))
simSData<-data.frame(simSData,sample(LETTERS[2:5],size=NCOL(simData),replace=TRUE),stringsAsFactors=FALSE)
colnames(simSData)<-c("A","B","C")
gSimData<-data.frame(sample(letters[2:5],size=NROW(simData),replace=TRUE),sample(2:5,size=NROW(simData),replace=TRUE))
gSimData<-data.frame(gSimData,sample(LETTERS[2:5],size=NROW(simData),replace=TRUE),stringsAsFactors=FALSE)
colnames(gSimData)<-c("a","b","c")

seSimData <- SummarizedExperiment(simData,colData=simSData,rowData=gSimData,metadata=mData)
seSimCount <- SummarizedExperiment(simCount,colData=simSData,rowData=gSimData,metadata=mData)

test<- clusterMany(simCount,reduceMethod="PCA",
    nReducedDims=c(5,10,50), 
    isCount=TRUE, verbose=FALSE,
    clusterFunction="pam", makeMissingDiss=TRUE,
    ks=2:4,
    findBestK=c(TRUE,FALSE))
						
test<-addClusterings(test,sample(2:5,size=NCOL(simData),replace=TRUE),clusterTypes="User")
clMatNew<-apply(clusterMatrix(test),2,function(x){
    wh<-sample(1:nSamples(test),size=10)
    x[wh]<- -1
    wh<-sample(1:nSamples(test),size=10)
    x[wh]<- -2
    return(x)
})

#make a new object with -1 values
ceSim<-ClusterExperiment(seSimCount,clMatNew,transformation=function(x){log2(x+1)})
clusterTypes(ceSim)<-clusterTypes(test)

ceSimData<-ClusterExperiment(seSimData,clMatNew,transformation=function(x){x})
clusterTypes(ceSimData)<-clusterTypes(test)

rm(test)
#################################
###small object based on simData/simCount (same size as trivial data)
### 15 samples from each of groups (including -2,-1)
###
#################################
whSamp<-unlist(tapply(1:nSamples(ceSim),primaryCluster(ceSim),function(x){sample(x,size=3)})) #15
smSimData<-simData[1:20,whSamp]
smSimCount<-simCount[1:20,whSamp]
smSimCE<-ceSim[1:20,whSamp]
smSimSE <- seSimData[1:20,whSamp]



#################################
###Make reduce dimensions and filters
#################################
sce<-as(se,"SingleCellExperiment")
sceFull<-sce
clusterExperiment:::filterStats(sceFull,type=c("Filter1","Filter2"))<-matrix(rnorm(2*nrow(sce)),ncol=2)
reducedDim(sceFull,type="Red1")<-matrix(rnorm(2*ncol(sce)),ncol=2)


sceSimData<-as(seSimData,"SingleCellExperiment")
sceSimDataDimRed<-sceSimData
pca_data <- prcomp(t(assay(sceSimData)),scale=TRUE,center=TRUE)
tsne_data <- matrix(rnorm(NCOL(sceSimData)*2),ncol=2)
reducedDims(sceSimDataDimRed) <- SimpleList(PCA=pca_data$x, TSNE=tsne_data)
clusterExperiment:::filterStats(sceSimDataDimRed,type=c("Filter1","Filter2"))<-matrix(rnorm(2*nrow(sceSimDataDimRed)),ncol=2)

#####################
## Create hdf5 SCE version
## Note is matrix of doubles....
#####################
hdfSCE<-HDF5Array::saveHDF5SummarizedExperiment(sceSimDataDimRed, dir="sceRedDem.h5", replace=TRUE)
hdfObj<-HDF5Array::saveHDF5SummarizedExperiment(sceSimData, dir="sce.h5", replace=TRUE)

###################
## Create cat stuff
###################
catMat <- matrix(sample(x=1:4,size=20*19,replace=TRUE),ncol=20)
catMat[1,1]<- -1 #force a negative value
colnames(catMat)<-paste("Sample",1:ncol(catMat))
rownames(catMat)<-paste("Gene",1:nrow(catMat))