R/splitbiopax_from_dt.R

In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

splitbiopax_from_dt<-
  function(biopax
           ,pwtoextract=NULL
           ,write_to_files=FALSE
           ,unifyids=TRUE
           
  ){
    #' @export
    #' @title
    #' Convert BioPAX Object to List of BioPAX Objects (by Pathway)
    #' @description 
    #' Splits a BioPAX object into a list of BioPAX objects by pathway. 
    #' Has an option of recording all of these BioPAX objects to files.
    #' @details 
    #' Returns a list of biopax objects.
    #' @param biopax BioPAX object.
    #' @param pwtoextract Vector of pathway ids. If \code{NULL} (default), all pathways are extracted.
    #' @param write_to_files Logical. Write to files? Default is \code{FALSE}.
    #' @param unifyids Logical. Unify IDs by making all elements of one class receive ids in the form "ClassNUMBER", 
    #' with NUMBER ranging from one to number of elements of such class? Default is \code{TRUE}.
    .
    
    #' @author 
    #' Ivan Grishagin
    
    #extract specified (or all) pathways from the biopax along with
    #all of their referenced instances 
    require(RIGbiopax)
    
    #pathways in the biopax
    bppws<-
      listPathways(biopax = biopax) %>%
      .$id
    
    if(is.null(pwtoextract)){
      pwtoextract<-
        bppws
    } else {
      pw_not_present<-
        pwtoextract[!pwtoextract %in% bppws]
      if(length(pw_not_present)>0){
        msg<-
          paste0("Some pathways could not be found in the biopax table:\n"
                 ,paste(pw_not_present
                        ,collapse="\n"))
        message(msg)
        #take only those pathways which are present in biopax
        pwtoextract<-
          pwtoextract[pwtoextract %in% bppws]
      }
    }
    #extract and store all biopax objects as a list
    splitbiopax_list<-
      pwtoextract %>%
      lapply(FUN=function(pwid){
        msg<-
          paste0("Processing pathway "
                 ,pwid
                 ," ("
                 ,match(pwid,pwtoextract)
                 ," of "
                 ,length(pwtoextract)
                 ,")"
          )
        message(msg)
        #select all instances referenced by a given pathway
        tempdf<-
          selectInstances(biopax = biopax
                          ,id = pwid
                          ,includeReferencedInstances = TRUE
                          ,biopaxlevel = 3)
        if(unifyids){
          tempdf<-
            tempdf %>%
            unify_biopax_ids(idtag=NULL)
        }
        #if not write to files,
        #filename is NULL
        #so the function will only return a biopax object
        if(!write_to_files){
          tempfilename<-
            NULL
        } else {
          tempfilename<-
            paste0(pwid
                   ,".owl")
        }
        tempbp<-
          biopax_from_dt(tempdf
                         ,filename=tempfilename)
        
        return(tempbp)
      })
    names(splitbiopax_list)<-
      pwtoextract
    
    return(splitbiopax_list)
  }