R/gene_bag_to_biopax.R

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

gene_bag_to_biopax<-
  function(gene_df=NULL
           ,filename=NULL
           ,cols=list(pwid="Pathway.ID"
                      ,pwname="Pathway.Name"
                      ,genedisplayname="Gene.Symbol"
                      ,genename="Gene.Name"
                      ,genesymbol="Gene.Symbol"
                      ,geneid="Gene.ID")
  ){
    #' @export
    #' @title
    #' Turn Set of Genes into BioPAX Object
    #' @description 
    #' Convert a dataframe containing a set of genes into a BioPAX object.
    #' @param gene_df Dataframe containing a set of genes.
    #' @param filename (optional) Output filename.
    #' If provided, a resultant BioPAX object will also be written to file.
    #' @param cols Names of the pertaining expected columns in \code{gene_df}.
    
    #' @author 
    #' Ivan Grishagin
    
    #ensure that gene_df is a dataframe
    gene_df<-
      gene_df %>%
      as.data.frame
    #declare list to store all biopax-style data table
    dTable_list<-
      list()
    #add unique gene name/display name combinations to the dataframe
    gene_df$cmbn<-
      paste0(gene_df[,cols$genedisplayname]
             ,gene_df[,cols$genename])
    
    #prepare component ids
    comp_ids<-
      paste(gene_df[,cols$pwid]
            ,unlist(lapply(unique(gene_df[,cols$pwid])
                           ,FUN = function(id){
                             #rows for given pw id
                             rows<-
                               (gene_df[,cols$pwid] %in% id)
                             #prepare indices for unique gene name/displayname
                             #combinations for given pw
                             ind<-
                               match(gene_df$cmbn[rows]
                                     ,unique(gene_df$cmbn[rows]))
                             return(ind)
                           }))
            ,"c"
            ,sep = "_")
    
    
    
    #references to the component names/xrefs/etc
    xref_ids<-
      paste0(comp_ids
             ,"x"
             ,internal_seq_along_find_reps(comp_ids))
    #references to db and id names
    db_ids<-
      paste0(xref_ids
             ,"x")
    
    #declare a biopax-style data table and fill pathway components
    dTable_list$dt_comp_ids<-
      data.frame(class="Pathway"
                 ,id=gene_df[,cols$pwid]
                 ,property="pathwayComponent"
                 ,property_attr="rdf:resource"
                 ,property_attr_value=comp_ids
                 ,property_value=""
      )
    #pathway names
    dTable_list$dt_pw_names<-
      data.frame(class="Pathway"
                 ,id=gene_df[,cols$pwid]
                 ,property="name"
                 ,property_attr="rdf:datatype"
                 ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                 ,property_value=gene_df[,cols$pwname]
      ) %>%
      unique
    #protein display names
    dTable_list$dt_prot_displaynames<-
      data.frame(class="Protein"
                 ,id=comp_ids
                 ,property="displayName"
                 ,property_attr="rdf:datatype"
                 ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                 ,property_value=gene_df[,cols$genedisplayname]
      )
    #protein names
    dTable_list$dt_prot_names<-
      data.frame(class="Protein"
                 ,id=comp_ids
                 ,property="name"
                 ,property_attr="rdf:datatype"
                 ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                 ,property_value=gene_df[,cols$genename]
      )
    
    #protein entity references
    dTable_list$dt_prot_refs<-
      data.frame(class="Protein"
                 ,id=comp_ids
                 ,property="entityReference"
                 ,property_attr="rdf:resource"
                 ,property_attr_value=xref_ids
                 ,property_value=""
      )
    
    #protein gene symbol
    dTable_list$dt_prot_refs_sym<-
      data.frame(class="ProteinReference"
                 ,id=xref_ids
                 ,property="name"
                 ,property_attr="rdf:datatype"
                 ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                 ,property_value=gene_df[,cols$genesymbol]
      )
    
    #protein entity references to the gene 
    dTable_list$dt_prot_refs_x<-
      data.frame(class="ProteinReference"
                 ,id=xref_ids
                 ,property="xref"
                 ,property_attr="rdf:resource"
                 ,property_attr_value=db_ids
                 ,property_value=""
      )
    
    #protein id db
    dTable_list$dt_prot_refs_x_db<-
      data.frame(class="RelationshipXref"
                 ,id=db_ids
                 ,property="db"
                 ,property_attr="rdf:datatype"
                 ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                 ,property_value="entrezgene"
      )
    
    #protein gene id
    dTable_list$dt_prot_refs_x_id<-
      data.frame(class="RelationshipXref"
                 ,id=db_ids
                 ,property="id"
                 ,property_attr="rdf:datatype"
                 ,property_attr_value="http://www.w3.org/2001/XMLSchema#string"
                 ,property_value=gene_df[,cols$geneid]
      )
    dTable<-
      do.call(rbind
              ,dTable_list) %>%
      unique
    
    biopax<-
      biopax_from_dt(dTable
                     ,filename=filename)
    
  }