R/make_plot_graph.R

In grishagin/RIGplotbiopax: Plot BioPAX Pathways

make_plot_graph<-
  function(allnodes
           ,alledges
           ,tag=NULL
           ,pw_name="Pathway"){  
    #' @export
    #' @title 
    #' Make and Plot BioPAX Graph
    #' @description 
    #' Using dataframes of nodes and edges make and plot the graph.
    #' @param allnodes Dataframe with all nodes.
    #' @param alledges Dataframe with all edges.
    #' @param tag Tag for the file name.
    #' @param pw_name Pathway name (optional). It will show up on-hover over the SVG background.
    #' 
    #' @author 
    #' Ivan Grishagin
    
    ########################################################
    #replace quotation marks with backticks to avoid error
    allnodes$label<-
      allnodes$label %>% 
      gsub("'|\""
           ,"`"
           ,.)
    
    pw_name<-
      pw_name %>% 
      gsub("'|\""
           ,"`"
           ,.)
    
    ########################################################
    #discover all nodes that link to dbid nodes
    dbid_ids<-
      allnodes[tooltip=="ID"]$id %>% 
      unique
    
    #find all nodes that refer to those dbid nodes
    to_dbid_df<-
      alledges[to %in% dbid_ids
               ,.(physent_id=paste0(from
                                    ,"OLD")
                  ,dbid_label=allnodes[id==to]$label)
               ,by=to]
    
    #remove dbid nodes from the allnodes and alledges
    allnodes<-
      allnodes[!id %in% dbid_ids]
    alledges<-
      alledges[!to %in% dbid_ids]
    
    ########################################################
    #since some nodes were removed, replace ids!
    #ensure that old ids have distinct names
    allnodes$id<-
      allnodes$id %>% 
      paste0("OLD")
    alledges$from<-
      alledges$from %>% 
      paste0("OLD")
    alledges$to<-
      alledges$to %>% 
      paste0("OLD")
    
    #make up a dictionary of replacements for nodes and edges
    #to ensure that nodes ids are the same as their row numbers
    node_id_dict<-
      data.frame(from=allnodes$id
                 ,to=1:nrow(allnodes))
    #replace char ids with int ids
    allnodes$id<-
      node_id_dict$to
    #replace edges ids
    alledges$id<-
      1:nrow(alledges)
    
    #now replace all edges references with integers, same as with nodes
    alledges$from<-
      alledges$from %>% 
      mapvalues(from=node_id_dict$from
                ,to=node_id_dict$to
                ,warn_missing = FALSE) %>% 
      as.integer
    alledges$to<-
      alledges$to %>% 
      mapvalues(from=node_id_dict$from
                ,to=node_id_dict$to
                ,warn_missing = FALSE) %>% 
      as.integer
    
    #replace all nodes referring to former dbid nodes
    to_dbid_df$physent_id<-
      to_dbid_df$physent_id %>% 
      mapvalues(from=node_id_dict$from
                ,to=node_id_dict$to
                ,warn_missing = FALSE) %>% 
      as.integer
    
    #prepare the final replacement dictionary 
    #to alter the svg string
    #to add attributes to xml tags
    to_dbid_df<-
      to_dbid_df[,.(from_tag=paste0("<g id=\"a_node"
                                    ,physent_id
                                    ,"\"")
                    ,to_tag=paste0("<g id=\"a_node"
                                   ,physent_id
                                   ,"\" class=\"clickable\" data-dbid=\""
                                   ,dbid_label
                                   ,"\""))]
    
    ########################################################
    #generate svg code via dot
    graph_svg<-
      #first, make diagrammer graph
      create_graph(nodes_df = allnodes
                   ,edges_df = alledges) %>% 
      add_global_graph_attrs("overlap", "false", "graph") %>% 
      delete_global_graph_attrs("layout","graph") %>% 
      add_global_graph_attrs("layout","dot","graph") %>% 
      add_global_graph_attrs("tooltip"
                             ,pw_name
                             ,"graph") %>% 
      #generate dot, then grviz code, and then svg string
      generate_dot %>% 
      grViz %>% 
      export_svg %>% 
      #replace selected node tags with their modified versions
      mgsub(pattern=to_dbid_df$from_tag
            ,replacement=to_dbid_df$to_tag
            ,text.var = .
            ,trim=FALSE)
    
    
    #save the file
    filename<-
      paste0(Sys.Date()
             ,"_"
             ,tag
             ,".svg")
    
    writeLines(graph_svg
               ,filename
               ,useBytes = TRUE)
    
  }