R/internal_nodes_physent.R

In grishagin/RIGplotbiopax: Plot BioPAX Pathways

internal_nodes_physent<-
  function(biopax){
    #' @keywords internal
    
    ######################## physical entities and node df
    node_physent_classes<-
      c("Pathway"
        ,"Protein"
        ,"Complex"
        ,"SmallMolecule"
        ,"PhysicalEntity"
        ,"RNA"
        ,"DNA"
      )
    
    #physical entity nodes with names
    physent_nodes<-
      biopax$dt[class %in% node_physent_classes &
                  property_value!=""
                ,.(label=paste(property_value
                               ,collapse="\n")
                   ,type=class)
                ,by=id] %>% 
      unique
    
    return(physent_nodes)
  }