R/internal_unite_mult_node_refs.R

In grishagin/RIGplotbiopax: Plot BioPAX Pathways

internal_merge_mult_node_refs<-
  function(nodes_edges_list
           ,ntype
           ,verbose=FALSE
           ,sep="|"){
    
    #' @keywords internal
    
    allnodes<-
      nodes_edges_list[[1]]
    alledges<-
      nodes_edges_list[[2]]
    
    alledges$newto<-NA_character_
    alledges[type %in% ntype]$newto<-
      alledges[type %in% ntype
               ,.(newto=paste0(from
                               ,paste(substr(ntype,1,2)
                                      ,collapse="")))]$newto
    
    #make up a dict of what to replace with what
    merge_dict<-
      alledges[type %in% ntype
               ,.(to
                  ,newto)]
    
    #and then replace those edges' from values
    alledges$from<-
      alledges$from %>% 
      mapvalues(from=merge_dict$to
                ,to=merge_dict$newto
                ,warn_missing = verbose) 
    
    alledges[!is.na(newto)]$to<-
      alledges[!is.na(newto)]$newto
    
    
    #replace allnodes id values...
    allnodes$id<-
      allnodes$id %>% 
      mapvalues(from=merge_dict$to
                ,to=merge_dict$newto
                ,warn_missing = verbose) 
    
    #...and merge their labels accordingly -- by id
    allnodes<-
      allnodes %>% 
      merge_cols_shorten_df(colKey = "id"
                            ,colsToMerge = "label"
                            ,patternToMerge = sep
                            ,return_other_cols=TRUE)
    
    return(list(allnodes=unique(allnodes)
                ,alledges=unique(alledges)))
  }