R/plot_pathways.R

In grishagin/RIGplotbiopax: Plot BioPAX Pathways

plot_pathways<-
  function(biopax
           ,pw_ids
           ,tag=NULL
           ,verbose=FALSE
           ,max_pw_size=10000){
    #' @export
    #' @title 
    #' Plot Pathways
    #' @description 
    #' Takes in a BioPAX object and pathway ids, and prepares plots in an SVG format.
    #' @param biopax A BioPAX object.
    #' @param pw_ids IDs of pathways to plot.
    #' @param tag Additional tag for the file name (optional).
    #' @param verbose Boolean. Show all warnings?
    #' @param max_pw_size Maximum allowed size of BioPAX data table. Defaults to 10,000. 
    #' If exceeded, pathway is split into several parts.
    #' 
    #' @author 
    #' Ivan Grishagin
    
    ####################################################################################################
    ######################## prepare biopax
    #strip hashes from the biopax property attr value column
    biopax$dt$property_attr_value<-
      biopax$dt$property_attr_value %>% 
      striphash
    
    ####################################################################################################
    #for each pathway, repeat
    for(pw_to_plot in pw_ids){
      message("Plotting pathway "
              ,pw_to_plot
              ,"...")
      #extract biopax instances just for a given pathway
      #and if there are any sub-pathways from inxight universe,
      #exclude references to all of their components to simplify things
      pw_biopax<-
        extract_pathways_from_biopax(biopax = biopax
                                     ,pw_ids = pw_to_plot
                                     ,exclude_subpw_comp_patt="inxight_pathways")
      
      if(is.null(pw_biopax)){
        next
      }else if(nrow(pw_biopax$dt)>max_pw_size){
        #split the pathway up roughly in chuncks of 10000 instances
        #will end up having more 
        #as some instances will be duplicated in each chunck
        Nchunks<-
          ceiling(nrow(pw_biopax$dt)/max_pw_size)
        
        pw_biopax_list<-
          pw_biopax %>% 
          split_pathway_into_chunks(pw_id=pw_to_plot
                                    ,Nchunks=Nchunks)
      }else{
        pw_biopax_list<-
          list(pw_biopax)
      }
      
      #clean-up to safely reuse the variable
      rm(pw_biopax)
      chunck_num<-0
      chunck_tag<-NULL
      
      for(pw_biopax in pw_biopax_list){
        #get pathway name
        pw_name<-
          pw_biopax$dt[id==pw_to_plot & 
                         grepl("name",tolower(property))][
                           order(-nchar(property_value))]$property_value[1]
        if(length(pw_biopax_list)>1){
          #count which part is being processed
          chunck_num<-
            chunck_num+1
          #make up the part name
          chunck_tag<-
            paste0("PART"
                   ,chunck_num
                   ,"of"
                   ,length(pw_biopax_list))
          
          #modify the pathway name (if more than one part present)
          #and inform the user
          pw_name<-
            pw_name %>% 
            paste(chunck_tag)
          
          message("\tProcessing "
                  ,chunck_tag
                  ,"...")
        }
        ####################################################################################################
        ######################## prepare all nodes and edges do the plotting
        if(verbose){
          allnodes_alledges<-
            make_allnodes_alledges(pw_biopax
                                   ,exclude_ids=pw_to_plot
                                   ,verbose=verbose)
          
          try(make_plot_graph(allnodes=allnodes_alledges$allnodes
                              ,alledges=allnodes_alledges$alledges
                              ,pw_name=pw_name
                              ,tag=paste0(pw_to_plot
                                          ,tag
                                          ,chunck_tag
                                          ,sep="_")))
        } else {
          suppressWarnings(
            allnodes_alledges<-
              make_allnodes_alledges(pw_biopax
                                     ,exclude_ids=pw_to_plot
                                     ,verbose=verbose))
          
          suppressWarnings(
            try(make_plot_graph(allnodes=allnodes_alledges$allnodes
                                ,alledges=allnodes_alledges$alledges
                                ,pw_name=pw_name
                                ,tag=paste(pw_to_plot
                                           ,tag
                                           ,chunck_tag
                                           ,sep="_"))))
        }
      }
      
    }
    
    return(NULL)
  }