R/internal_edges_ctrl.R

In grishagin/RIGplotbiopax: Plot BioPAX Pathways

internal_edges_ctrl<-
  function(biopax){
    #' @keywords internal
    
    edges<-list()
    
    ######################## controls df
    node_control_classes<-
      biopax$dt[property %in% c("controller"
                                ,"controlled"
                                ,"controlType")]$class %>% 
      unique
    
    #get df of controller and controlled components
    controls_df<-
      biopax$dt[class %in% node_control_classes
                ,.(cer=property_attr_value[property=="controller"]
                   ,ced=property_attr_value[property=="controlled"]
                   ,ct=property_value[property=="controlType"]
                   ,catdir=property_value[property=="catalysisDirection"]
                   ,xref=property_attr_value[property=="xref"]
                   ,evidence=property_attr_value[property=="evidence"]
                )
                ,by=id]
    
    if(nrow(controls_df)<1){
      return(NULL)
    }
    
    #find the ids that the evidence ids are referring to, and merge them using ; as separator
    #the reason's that vocabulary function will refer evidence ids to the control components
    #whereas we are excluding them from being physical nodes
    controls_df$evidence<-
      controls_df$evidence %>% 
      lapply(FUN=function(pid){
        getReferencedIDs(biopax=biopax
                         ,id=pid
                         ,recursive=FALSE)
      }) %>% 
      sapply(paste,collapse=";")
    
    #lengthen df by splitting those combined ids (likely not needed but just in case)
    controls_df<-
      controls_df %>% 
      split_cols_lengthen_df(colsToSplit = "evidence"
                             ,patternToSplit = ";"
                             ,at_once = FALSE)
    
    
    
    #split up catalysis direction by dash
    controls_df<-
      controls_df %>% 
      split_col_widen_df(colToSplit = "ct"
                         ,split = "-"
                         ,newcolnames = c("type"
                                          ,"label")) 
    
    controls_df[is.na(type)]$type<-
      "UNKNOWNCTRL"
    
    # controllers to controlled edges
    edges$cer2ced_df<-
      controls_df[!is.na(cer) &
                    !is.na(ced)][,.(from=cer
                                    ,to=ced
                                    ,type
                                    ,label)]
    
    # controlleds to xref edges
    edges$ced2dbid_df<-
      controls_df[!is.na(xref) &
                    !is.na(ced)][,.(from=ced
                                    ,to=xref
                                    ,type="dbid")]
    # controllers to xref edges
    # for when the controlleds are NA
    edges$cer2dbid_df<-
      controls_df[!is.na(xref) &
                    !is.na(cer) &
                    is.na(ced)][,.(from=cer
                                   ,to=xref
                                   ,type="dbid")]
    
    # controlleds to evidence edges
    edges$ced2ev_df<-
      controls_df[!is.na(evidence) &
                    !is.na(ced)][,.(from=ced
                                    ,to=evidence
                                    ,type="Evidence")] 
    # controllers to evidence edges
    # for when the controlleds are NA
    edges$cer2ev_df<-
      controls_df[!is.na(evidence) &
                    !is.na(cer) &
                    is.na(ced)][,.(from=cer
                                   ,to=evidence
                                   ,type="Evidence")]
    
    alledges<-
      edges %>% 
      do.call(rbind.fill
              ,.) %>% 
      unique
    
    return(alledges)
  }