R/internal_edges_dbid.R

In grishagin/RIGplotbiopax: Plot BioPAX Pathways

internal_edges_dbid<-
  function(biopax){
    #' @keywords internal
    
    dbid_ids<-
      biopax$dt[property %in% c("id","db")]$id %>% 
      unique
    
    #all entities to dbid edges
    all2dbid_edges<-
      biopax$dt[property_attr_value %in% dbid_ids
                ,.(from=id
                   ,to=property_attr_value
                   ,class
                   ,type="dbid")]
    
    #for all those edges that have a class with a word "reference" in it
    #we need to find instances that refer to them, and replace those "from" ids
    #i.e. get the id of the object referring to the xref, i.e. the actual physical entity
    #get those rows as a logical vector
    refs_logi<-
      grepl("reference"
            ,all2dbid_edges$class
            ,ignore.case = TRUE)
    
    #get all those ids and combine them using ; as separator
    all2dbid_edges[refs_logi]$from<-
      all2dbid_edges[refs_logi]$from %>% 
      lapply(FUN=function(pid){
        getReferencingIDs(biopax=biopax
                          ,id=pid
                          ,recursive=FALSE)
      }) %>% 
      sapply(paste,collapse=";")
    
    #remove auxiliary class column
    all2dbid_edges$class<-NULL
    
    #lengthen df by splitting those combined ids
    all2dbid_edges<-
      all2dbid_edges %>% 
      split_cols_lengthen_df(colsToSplit = "from"
                             ,patternToSplit = ";")
    
    return(all2dbid_edges)
  }