R/load_biopax_pathways.R

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

load_biopax_pathways<-
  function(owl_biopax=NULL){
    
    #' @export
    #' @title 
    #' Load BioPAX Pathways From BioPAX Object
    #' @description 
    #' Extracts all pathways from a BioPAX Object.
    #' @param owl_biopax A BioPAX object.
    #' 
    #' @author 
    #' Ivan Grishagin
    
    
    if(is.null(owl_biopax)){
      stop("Biopax object was not provided")
    }
    name_properties<-
      grep("name", owl_biopax$dt$property,ignore.case = TRUE, value = TRUE) %>% 
      unique() %>%
      tolower
    
    #pathway names are indicated in different biopax sources in a different manner
    #sometimes they are presented as standard name and name
    #and when they don't coincide, such "standardnames" are just GO processes
    if ("displayname" %in% name_properties) {
      #get instances of displayName of class pathway
      owl_biopax_instances_stname<-
        selectInstances(biopax=owl_biopax,
                        class="pathway",
                        property="displayName") 
      
      #subset a standardname df, select id and property columns
      pw_biopax<-
        owl_biopax_instances_stname %>%
        dplyr::select(id, name=property_value)
    } else if("standardname" %in% name_properties & 
              "name" %in% name_properties ){
      #get instances of name and standardname of class pathway
      owl_biopax_instances_stname<-
        selectInstances(biopax=owl_biopax,
                        class="pathway",
                        property="standardName") 
      
      owl_biopax_instances_name<-
        selectInstances(biopax=owl_biopax,
                        class="pathway",
                        property="name")
      
      #instances of standrdname with same id as name
      matching_rows<-
        owl_biopax_instances_stname$id %in% owl_biopax_instances_name$id
      #subset a standardname df, select id and property columns
      pw_biopax<-
        owl_biopax_instances_stname[matching_rows,] %>%
        dplyr::select(id, name=property_value)
    } else if ("name" %in% name_properties) {
      #get instances of name of class pathway
      owl_biopax_instances_stname<-
        selectInstances(biopax=owl_biopax,
                        class="pathway",
                        property="name") 
      
      #subset a standardname df, select id and property columns
      pw_biopax<-
        owl_biopax_instances_stname %>%
        dplyr::select(id, name=property_value)
    } else {
      stop("load_biopax_pathways: check your name properties!")
    }
    
    #if pw_biopax is still empty, try default rBiopaxParser function
    if (nrow(pw_biopax)<1){
      pw_biopax<-
        listPathways(owl_biopax)
    }
    
    #convert names to lower case
    pw_biopax$name<-tolower(pw_biopax$name)
    
    #change colnum names
    colnames(pw_biopax)<-c("biopax.Pathway.ID","biopax.Pathway.Name")
    
    return(pw_biopax)
  }