R/uniqueGroupHclust.R

In HCgglasso: Group-Lasso with Hierarchical Clustering

#' Find all unique groups in \code{\link{hclust}}  results
#'
#' @author Quentin Grimonprez
#' @param hc output of \code{\link{hclust}}  function
#' @return A list containing :
#' \describe{
#'   \item{indexGroup}{Vector containing the index of variables.}
#'   \item{varGroup}{Vector containing the index of the group of each variable.}
#' }
#'
#' @examples 
#' hc <- hclust(dist(USArrests), "ave")
#' res <- uniqueGroupHclust(hc)
#' 
#' 
#' @export
uniqueGroupHclust=function(hc)
{
  #check if hc is a hclust object
  if(class(hc)!="hclust")
    stop("hc must be an hclust object.")
  
  #hc$merge contains the order and composition (2 number) of the different merge 
  nr=nrow(hc$merge)
  ind=1:(nr+1)
  gr=1:(nr+1)

  #for each merge (=level of hierarchical clustering)
  for(i in 1:nr)
  {
    #positive number = number of the line of the cluster merged
    #negative number = single variable
    
    indpos=which(hc$merge[i,]>0)
    pos=hc$merge[i,indpos]
    neg=abs(hc$merge[i,][hc$merge[i,]<0])
    
    #for each cluster, search the variables it contains
    while(length(pos)>0)
    {   
      pos=hc$merge[pos,]
      neg=c(neg,abs(pos[pos<0]))
      pos=pos[pos>0]
    }
    
    #complete output
    ind=c(ind,sort(neg)) 
    gr=c(gr,rep(i+nr+1,length(neg)))
    
  }#fin for row merge 
  
  return(list(varGroup=ind,indexGroup=gr))
}