R/pplace_to_table.R

In BoSSA: A Bunch of Structure and Sequence Analysis

pplace_to_table <-
function(pplace,type="full",run_id=NULL){
  if(class(pplace)!="pplace"){
    stop("ERROR: the input is not an object of class pplace")
  }
  if(!is.null(run_id)){
    pplace <- sub_pplace(pplace,run_id=run_id)
  }
  out <- NULL
  if(nrow(pplace$multiclass)>0){
    out <- merge(pplace$multiclass,pplace$placement_positions,by="placement_id")
    if(type=="best"){
      out <- out[order(out$ml_ratio,decreasing=TRUE),]
      out <- out[match(unique(out$placement_id),out[,1]),]
    }
    out <- out[order(out$placement_id),]
    rownames(out) <- NULL
    colnames(out)[c(5,12)] <- c("tax_id_multilcass","tax_id_placement")
  }
  return(out)
}