R/helpers.r

In Biclustering/biclust: BiCluster Algorithms

#### Littel Helper Functions for preprocessing the Data ########


#### discretize: Discretize a Matrix to wished levels ############
discretize<-function(x,nof=10,quant=FALSE){
res<-x
ni<-dim(x)[1]
nj<-dim(x)[2]


if(quant)
{
levels<-quantile(x,seq(0+1/nof,1,by=1/nof))
}
else
{
mindat<-min(x)
maxdat<-max(x)
levels<-vector('integer',length=nof)
diff<-(maxdat-mindat)/nof

for(k in 1:nof)
  {
  levels[k]<-mindat+ k*diff
  }
}

for(i in 1:ni)
  {
  for(j in 1:nj)
    {
    for(k in 1:nof)
    if(x[i,j] <= levels[nof-k+1])
      {res[i,j]<-k}
    }
  }
res
}


prequest<-function(mat, level=0,method=c('sd','mean1','mean2'))
{
if(method=="sd")
{
val<-apply(mat,2,sd)
ident<-val>level
return(list(mat[ident,],ident))
}
if(method=="mean1")
{
dat<-mat-apply(mat,2,mean)
val<-rowSums(dat)
ident<-val>=level
}
if(method=="median")
{
dat<-mat!=apply(mat,2,median)
val<-rowSums(dat)
ident<-val>=level
}
else
{
print("Wrong method")
}
}  
  
###### Little Helper functions for analysing the Results



##Funktion zur Ausgabe eines Biclusters

writeclust<-function(Biclusterresult,row=TRUE,noC=10){


  if(row){

    x<-rep(0,dim(Biclusterresult@RowxNumber)[1])
    for (i in 1:min(Biclusterresult@Number,noC)){
      x<-x+i*Biclusterresult@RowxNumber[,i]
    }
  }
  else {
    x<-rep(0,dim(Biclusterresult@NumberxCol)[2])
    for (i in 1:min(Biclusterresult@Number,noC)){
      x<-x+i*Biclusterresult@NumberxCol[i,]
    }
  }
  x
}


plotclust <- function(res,x,bicluster=TRUE,legende=FALSE,noC=5,wyld=3,Titel="Plotclust",...)
{

if(bicluster)
  {
  op<-par(mfrow=c(3,2))

  for ( i in 1:min(res@Number,noC))
    {
    identq <- res@NumberxCol[i,]
    identper <- res@RowxNumber[,i]
    anz<-sum(identper)
    le <- sum(identq)
    if (anz == 0){
      break
     }


    mat <- matrix(0,3,le)
    mat[1,] <- colMeans(x[identper,identq])
    mat[2,] <- colMeans(x[!identper,identq])
    mat[3,] <- apply(x[!identper,identq],2,median)
    rownames(mat) <- c("Value","Mean","Median")
    colnames(mat) <- colnames(x[,identq])
    if(legende)
      {
      barplot(mat,beside=T,legend=rownames(mat),main=paste("Cluster",i,"Size:",anz),ylim=c(min(0,min(mat)),(max(5,max(mat)+3))),las=wyld,...)
      }
    else
      {
      barplot(mat,beside=T,main=paste("Cluster",i,"Size:",anz),las=wyld,...)
      }
    }
  par(op)
  }

else
  {
  op<-par(mfrow=c(3,2))

  for ( i in 1:min(length(res$size),noC)){
    identper <- res$cluster==i
    anz<-sum(identper)
    if (anz == 0){
      break
     }


    mat <- matrix(0,3,dim(x)[2])
    mat[1,] <- colMeans(x[identper,])
    mat[2,] <- colMeans(x[!identper,])
    mat[3,] <- apply(x[!identper,],2,median)
    rownames(mat) <- c("Value in Bicluster","Mean in remaining ","Median")
    colnames(mat) <- colnames(x)
        if(legende)
      {
      barplot(mat,beside=T,legend=rownames(mat),main=paste("Cluster",i,"Size:",anz),ylim=c(min(0,min(mat)),(max(5,max(mat)+3))),las=wyld,...)
      }
    else
      {
      barplot(mat,beside=T,main=paste("Cluster",i,"Size:",anz),las=wyld,...)
      }
    }
  
  par(op)
  }
title(Titel)
}

# Converts a Biclust object to a list of bicluster objects
# A bicluster object has rows and cols fields
# Each one is a list of numbers that represents the rows and columns in the bicluster
# in the same order that they appear in the Biclust object (that is, the order of the original matrix)
# bicResult is a Biclust object
convertclust=function(bicResult)
{
	setClass("bicluster", representation(rows="integer", cols="integer"))
	
	if(class(bicResult)!="Biclust")
		{
		stop("The argument 'bicResult' must be of class Biclust")
		}
	biclusters=c()
	for (i in 1:(bicResult@Number)) 
	{
		listar = which(bicResult@RowxNumber[,i])
		listac = which(bicResult@NumberxCol[i,])
		if(length(listar)==0 || length(listac)==0)	{}
		else{
			bic=new("bicluster")
			bic@rows=listar
			bic@cols=listac
			biclusters=c(biclusters,bic)
		}
	}	
	biclusters
}


#Takes a list of biclusters and returns a list of the largest maxNumber biclusters
#with less overlap than "overlapThreshold"  (or a number < maxNumber if there are not enough biclusters
#that satisfy the overlap criterium). maxNumber default is 100.
# overlapThreshold must be in [0,1], representing the percentage of overlap (default 0.25)
# bics is a list of "bicluster" objects
filterclust=function(bics, overlapThreshold=0.25, maxNumber=100)
{
	cont=0
	sizes=as.numeric(lapply(1:length(bics), function(i) length(bics[[i]]@rows)*length(bics[[i]]@cols)))
	bics2=c()
	for(i in bics[order(sizes, decreasing=T)])
	{
		if(cont>=maxNumber)	break
		insert=T
		for(j in bics2)
		{
			if(overlap(i,j)>=overlapThreshold)
			{
				insert=F
				break
			}
		}
		if(insert)	
		{
			bics2=c(bics2,i)
			cont=cont+1
		}
	}
	bics2
}

#Returns the amount of overlap between two biclusters, measured in terms of 
#percentage respect to bic1 (bic1 and bic2 are bicluster objects with fields rows and cols)
overlap=function(bic1,bic2)
{
	length(intersect(bic1@rows,bic2@rows))/length(bic1@rows)*length(intersect(bic1@cols,bic2@cols))/length(bic1@cols)	
}