R/SharedSelection.R

In IntClust: Integrated Data Analysis via Clustering

SharedSelection<-function(DataLimma=NULL,DataMLP=NULL,DataFeat=NULL,names=NULL){  #Input=result of DiffGenes.2 and Geneset.intersect
	if(is.null(DataLimma) & is.null(DataMLP) & is.null(DataFeat)){	
		stop("At least one Data set should be specified")
	}
	
	List=list(DataLimma,DataMLP,DataFeat)
	AvailableData=sapply(seq(length(List)),function(i) if(!(is.null(List[[i]]))) return(i))
	AvailableData=unlist(AvailableData)
	len=c()
	for(i in AvailableData){
		len=c(len,length(List[[i]]))
	}
	if(length(unique(len))!=1){
		stop("Unequal number of methods for limma and MLP")
	}
	else{
		DataSets=lapply(AvailableData,function(i)  return(List[[i]]))
		nmethods=length(DataSets[[1]])
		#nclusters=length(DataSets[[1]][[1]])
	}
	
	if(is.null(names)){
		for(j in 1:nmethods){
			names[j]=paste("Method",j,sep=" ")	
		}
	}
	
	which=list()	
	table=c()
			
	comps=c()
	
	temp1g=c()
	temp1p=c()
	temp1f=list()
		
	for (i in 1:nmethods){			
			
		if(!(is.na(DataSets[[1]][[i]])[1])){
			comps=c(comps,length(DataSets[[1]][[i]]$Compounds$LeadCpds))
			names(comps)[i]=paste("Ncomps", names[i],sep=" ")
		}
		else{
			comps=c(comps,"-")
		}
		
		if(!(is.null(DataLimma))){
			if(!(is.na(DataLimma[[i]])[1])){
				temp1g=c(temp1g,length(DataLimma[[i]]$Genes$TopDE$ID))
			}
			else{
				temp1g=c(temp1g,"-")
			}	
			names(temp1g)[i]=names[i]
		}
		else{
			temp1g=NULL
		}
		
		if(!(is.null(DataMLP))){
			if(!(is.na(DataMLP[[i]])[1])){
				temp1p=c(temp1p,length(DataMLP[[i]][[3]]$geneSetDescription))
			}
			else{
				temp1p=c(temp1g,"-")
			}	
			names(temp1p)[i]=names[i]
		}
		else{
			temp1p=NULL
		}
		
		if(!(is.null(DataFeat))){
			temp=c()
			for(f in 1:length(DataFeat[[i]]$Characteristics)){			
				if(!(is.na(DataFeat[[i]])[1])){
					temp=c(temp,length(DataFeat[[i]]$Characteristics[[f]]$TopFeat$Names))
				}
				else{
					temp=c(temp,"-")
				}
				
				names(temp)[f]=names(DataFeat[[i]]$Characteristics)[f]
			}	
			temp1f[[i]]=temp
			names(temp1f)[i]=names[i]	
		}
		else{
			temp1f=NULL
		}
			
		if (i==1){
			cont=c()
			for(d in 1:length(DataSets)){
				cont=c(cont,!(is.na(DataSets[[d]][[i]])[1]))
			}	
			
			if(any(cont)){
				
				sharedcomps=DataSets[[1]][[i]]$Compounds$LeadCpds
				nsharedcomps=length(sharedcomps)
				names(nsharedcomps)="Nsharedcomps"
				
				
				if(!(is.null(DataLimma))){
					sharedgenes=DataLimma[[i]]$Genes$TopDE$ID
					nsharedgenes=length(sharedgenes)
					names(nsharedgenes)="Nshared"
				}
				else{
					sharedgenes=NULL
					nsharedgenes=0
				}
				
				
				if(!(is.null(DataMLP))){
					sharedpaths=DataMLP[[i]][[3]]$geneSetDescription
					nsharedpaths=length(sharedpaths)
					names(nsharedpaths)="Nshared"
					
				}
				else{
					sharedpaths=NULL
					nsharedpaths=0
				}
				if(!(is.null(DataFeat))){
					sharedfeat=list()
					nsharedfeat=list()
					for(f in 1:length(DataFeat[[i]]$Characteristics)){	
						sharedfeat[[f]]=DataFeat[[i]]$Characteristics[[f]]$TopFeat$Names	
						names(sharedfeat)[f]=paste("Shared: ",names(DataFeat[[1]]$Characteristics)[f],sep="")
						
						nsharedfeat[[f]]=length(sharedfeat[[f]])
						names(nsharedfeat)[f]=paste("Nshared: ",names(DataFeat[[1]]$Characteristics)[f],sep="")
											
					}
					
				}
				else{
					sharedfeat=NULL
					nsharedfeat=0
				}
			}		
		}
		else{	
				
			sharedcomps=intersect(sharedcomps,DataSets[[1]][[i]]$Compounds$LeadCpds)
			nsharedcomps=length(sharedcomps)
			names(nsharedcomps)="Nsharedcomps"
			
			
			if(!(is.null(DataLimma))){
				sharedgenes=intersect(sharedgenes,DataLimma[[i]]$Genes$TopDE$ID)
				nsharedgenes=length(sharedgenes)
				names(nsharedgenes)="Nshared"
				
			}
			if(!(is.null(DataMLP))){
				sharedpaths=intersect(sharedpaths,DataMLP[[i]][[3]]$geneSetDescription)
				nsharedpaths=length(sharedpaths)
				names(nsharedpaths)="Nshared"
				
			}
			if(!(is.null(DataFeat))){
				
				for(f in 1:length(DataFeat[[i]]$Characteristics)){	
					sharedfeat[[f]]=intersect(sharedfeat[[f]],DataFeat[[i]]$Characteristics[[f]]$TopFeat$Names)	
					names(sharedfeat)[f]=paste("Shared: ",names(DataFeat[[1]]$Characteristics)[f],sep="")
					
					nsharedfeat[[f]]=length(sharedfeat[[f]])
					names(nsharedfeat)[f]=paste("Nshared: ",names(DataFeat[[i]]$Characteristics)[f],sep="")
					
					
				}
				
			}
		}
	}
		
	pvalsgenes=list()
	meanpvalsgenes=c()
	
	pvalspaths=list()
	meanpvalspaths=c()
	
	pvalsfeat=list()
	meanpvalsfeat=c()
	
	
	if(!(is.null(sharedgenes)) & nsharedgenes != 0 ){
		for(c in 1:nmethods){
			pvalsg=c()
			for(g in sharedgenes){
				if(!(is.na(DataLimma[[c]])[1])){
					pvalsg=c(pvalsg,DataLimma[[c]]$Genes$TopDE$adj.P.Val[DataLimma[[c]]$Genes$TopDE$ID==g])	
				}	
			}
			
			pvalsgenes[[c]]=pvalsg
			names(pvalsgenes)[c]=paste("P.Val.",names[c],sep="")
		}	
		
		for(g1 in 1:length(sharedgenes)){
			pvalstemp=c()			
			for(c in 1:nmethods){
				if(!(is.na(DataLimma[[c]])[1])){
					pvalstemp=c(pvalstemp,pvalsgenes[[c]][[g1]])
				}
			}			
			meanpvalsgenes=c(meanpvalsgenes,mean(pvalstemp))			
		}
		pvalsgenes[[nmethods+1]]=meanpvalsgenes	
		names(pvalsgenes)[nmethods+1]="Mean pvals genes"
	}
	else{
		pvalsgenes=NULL
		nsharedgenes=NULL
	}
	
	if(!(is.null(sharedpaths)) & nsharedpaths != 0){
		for(c in 1:nmethods){
			pvalsp=c()
			if(!(is.na(DataMLP[[c]])[1])){
				for(p in sharedpaths){
					pvalsp=c(pvalsp,DataMLP[[c]][[3]][DataMLP[[c]][[3]]$geneSetDescription==p,5][1])
				}
			}
			
			pvalspaths[[c]]=pvalsp
			names(pvalspaths)[c]=paste("P.Val.",names[c],sep="")
		}
		
		
		for(p1 in 1:length(sharedpaths)){
			pvalstemp1=c()
			for(c in 1:nmethods){
				if(!(is.na(DataMLP[[c]])[1])){
					pvalstemp1=c(pvalstemp1,pvalspaths[[c]][[p1]])
					
				}
				
			}			
			
			meanpvalspaths=c(meanpvalspaths,mean(pvalstemp1))
		}
		pvalspaths[[nmethods+1]]=meanpvalspaths	
		names(pvalspaths)[nmethods+1]="Mean pvals paths"
	}
	else{
		pvalpaths=NULL
		nsharedpaths=NULL
	}
	
	if(!(is.null(sharedfeat)) & !(is.null(Reduce("+",nsharedfeat)))){
		for(f in 1:length(DataFeat[[1]]$Characteristics)){
			pvalschar=list()
			for(c in 1:nmethods){
				pvalsf=c()
				if(!(is.na(DataFeat[[c]])[1])){
					for(s in sharedfeat[[f]]){
						pvalsf=c(pvalsf,DataFeat[[c]]$Characteristics[[f]]$TopFeat$adj.P.Val[DataFeat[[c]]$Characteristics[[f]]$TopFeat$Names==s])
					}
				}
				
				pvalschar[[c]]=pvalsf
				names(pvalschar)[c]=paste("P.Val.",names[c],sep="")				
			}
			pvalsfeat[[f]]=pvalschar
			names(pvalsfeat)[f]=names(DataFeat[[1]]$Characteristics)[f]
			
		}
		
		for(f in 1:length(DataFeat[[1]]$Characteristics)){
			meanpvalsfeat=c()
			for(f1 in 1:length(sharedfeat[[f]])){
				pvalstemp=c()			
				for(c in 1:nmethods){
					if(!(is.na(DataFeat[[c]])[1]) & pvalsfeat[[f]]){
						pvalstemp=c(pvalstemp,pvalsfeat[[f]][[c]][[f1]])
					}
				}			
				meanpvalsfeat=c(meanpvalsfeat,mean(pvalstemp))			
			}
			
			pvalsfeat[[f]][[nmethods+1]]=meanpvalsfeat
			names(pvalsfeat[[f]])[nmethods+1]="Mean pvals feat"
		}
		lenchar=length(DataFeat[[1]]$Characteristics)
		
	}
	else{
		if(is.null(sharedfeat)){
			pvalsfeat=NULL
			nsharedfeat=NULL
			lenchar=0
		}
		else if(!(is.null(sharedfeat))){
			pvalsfeat=NULL
			lenchar=lenchar=length(DataFeat[[1]]$Characteristics)
		}
	}
		
	if(!(is.null(temp1f))){
		temp1f=do.call(rbind.data.frame, temp1f)	
		colnames(temp1f)=names(DataFeat[[1]]$Characteristics)
		temp1f=as.matrix(temp1f)
		nsharedfeat=do.call(cbind.data.frame, nsharedfeat)
		nsharedfeat=as.matrix(nsharedfeat)
	}
	part1=cbind(cbind(temp1g,temp1p),temp1f)
	part1=as.matrix(part1)
	if(is.null(nsharedgenes) | is.null(nsharedpaths)  | is.null(nsharedfeat)){
		if(!(is.null(temp1g))){
			nsharedgenes=0
		}
		if(!(is.null(temp1p))){
			nsharedpaths=0
		}
		if(!(is.null(temp1f))){
			nsharedfeat=rep(0,length(temp1f))
		}
	}
	part2=cbind(cbind(nsharedgenes,nsharedpaths),nsharedfeat)
	part2=as.matrix(part2)
	rownames(part2)="NShared"
	#print(str(part2))
	colnames(part1)=NULL
	colnames(part2)=NULL
	
	part3=c()
	for(r in 1:length(comps)){
		part3=rbind(part3,rep(comps[r],dim(part1)[2]))
	}
	colnames(part3)=NULL
	rownames(part3)=names(comps)
	part4=rep(nsharedcomps,dim(part1)[2])
	names(part4)=NULL
	temp=rbind(part1,part2,part3,part4)	
	rownames(temp)[nrow(temp)]="Nsharedcomps"
	
	
	table=cbind(table,temp)
	colnames(table)=seq(1,ncol(table))
	
	if(!(is.null(pvalsgenes))){
		SharedGenes=cbind(SharedGenes=sharedgenes,do.call(cbind.data.frame, pvalsgenes))
	}
	else{
		SharedGenes=NULL
	}
	if(!(is.null(pvalspaths))){
		SharedPaths=cbind(SharedPaths=sharedpaths,do.call(cbind.data.frame, pvalspaths))
	}
	else{
		SharedPaths=NULL
	}
	if(!(is.null(pvalsfeat))){
		SharedFeat=list()
		for(f in 1:lenchar){
			SharedFeat[[f]]=cbind(SharedFeat=sharedfeat[[f]],do.call(cbind.data.frame, pvalsfeat[[f]]))
			names(SharedFeat)[f]=names(pvalsfeat)[f]
		}
	}
	else{
		SharedFeat=NULL
	}
	
	which[[1]]=list(SharedComps=sharedcomps,SharedGenes=SharedGenes,SharedPaths=SharedPaths,SharedFeat=SharedFeat)
	names(which)[1]="Selection"
	
	#Sep for all situations?
	if(all(!(is.null(DataLimma)),!(is.null(DataMLP)),!(is.null(DataFeat)))){
		for (i in 1:length(seq(1,dim(table)[2],lenchar+2))){
			number=seq(1,dim(table)[2],2+lenchar)[i]
			colnames(table)[number]=paste("G.Cluster",sep=" ")	
			colnames(table)[number+1]=paste("P.Cluster",sep=" ")	
			for(u in seq(1:lenchar)){
				colnames(table)[number+1+u]=paste(paste('Feat.',names(DataFeat[[1]]$Characteristics)[u],sep=""),paste(".Cluster",sep=" "),sep="")
			}
			
		}
	}	
	
	else if(all(!(is.null(DataLimma)),!(is.null(DataMLP)),is.null(DataFeat))){
		for (i in 1:length(seq(1,dim(table)[2],2))){
			number=seq(1,dim(table)[2],2)[i]
			colnames(table)[number]=paste("G.Cluster",i,sep=" ")	
			colnames(table)[number+1]=paste("P.Cluster",i,sep=" ")	
			
		}
	}	
	
	else if(all(!(is.null(DataLimma)),is.null(DataMLP),!(is.null(DataFeat)))){
		for (i in 1:length(seq(1,dim(table)[2],lenchar+1))){
			number=seq(1,dim(table)[2],1+lenchar)[i]
			colnames(table)[number]=paste("G.Cluster",i,sep=" ")	
			for(u in seq(1:lenchar)){
				colnames(table)[number+u]=paste(paste('Feat.',names(DataFeat[[1]]$Characteristics)[u],sep=""),paste(".Cluster",i,sep=" "),sep="")
			}
			
		}
	}
	
	else if(all((is.null(DataLimma)),!(is.null(DataMLP)),!(is.null(DataFeat)))){
		for (i in 1:length(seq(1,dim(table)[2],lenchar+1))){
			number=seq(1,dim(table)[2],lenchar+1)[i]	
			colnames(table)[number]=paste("P.Cluster",i,sep=" ")	
			for(u in seq(1:lenchar)){
				colnames(table)[number+u]=paste(paste('Feat.',names(DataFeat[[1]]$Characteristics)[u],sep=""),paste(".Cluster",i,sep=" "),sep="")
			}
			
		}
	}	
	
	else if(all(!(is.null(DataLimma)),(is.null(DataMLP)),(is.null(DataFeat)))){
		for (i in 1:length(seq(1,dim(table)[2],1))){
			colnames(table)[i]=paste("G.Cluster",sep=" ")				
		}
	}	
	
	else if(all((is.null(DataLimma)),!(is.null(DataMLP)),(is.null(DataFeat)))){
		for (i in 1:length(seq(1,dim(table)[2],1))){
			colnames(table)[i]=paste("P.Cluster",sep=" ")				
		}
	}	
	
	else if(all((is.null(DataLimma)),(is.null(DataMLP)),!(is.null(DataFeat)))){
		for (i in 1:length(seq(1,dim(table)[2],lenchar))){
			number=seq(1,dim(table)[2],2)[i]
			for(u in c(0,1)){
				colnames(table)[number+u]=paste(paste('Feat.',names(DataFeat[[1]]$Characteristics)[u+1],sep=""),paste(".Cluster",sep=" "),sep="")
			}
			
		}
	}	
	
		
	
	ResultShared=list(Table=table,Which=which)
	return(ResultShared)
		
	
}