R/internal_analyse_toxdb_biopax_results_df.R

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

internal_analyse_toxdb_biopax_results_df<-
  function(dFrame
           ,label=NULL){
    
    #' @keywords internal
    
    #make a summary
    summary_df<-
      dFrame %>%
      #group by pathway id, then genematch
      dplyr::group_by(toxdb.Pathway.ID,.genematch) %>%
      dplyr::summarise(count=n()) %>%
      spread(key = .genematch
             ,value = count) %>%
      dplyr::mutate(total_toxdb=sum(`1_match`
                                    ,`2_toxdb`
                                    ,na.rm=TRUE)
                    ,total_biopax=sum(`1_match`
                                      ,`3_biopax`
                                      ,na.rm=TRUE)
                    ,`matches_toxdb,%`=
                      round(100*`1_match`/total_toxdb,0) 
                    ,`misses_toxdb,%`=
                      round(100*`2_toxdb`/total_toxdb,0)
                    ,`matches_biopax,%`=
                      round(100*`1_match`/total_biopax,0)
                    ,`extra_biopax,%`=
                      round(100*`3_biopax`/total_biopax,0)
      ) 
    #replace NA with 0
    summary_df[is.na(summary_df)]<-0
    
    #arrange by misses_toxdb
    summary_df<-
      summary_df %>%
      dplyr::arrange(`matches_toxdb,%`
                     ,`matches_biopax,%`
                     ,`extra_biopax,%`)
    
    #fix colnames
    colnames(summary_df)[2:4]<-
      c("matches"
        ,"misses_toxdb"
        ,"extra_biopax")
    
    #write to file
    write.xlsx(summary_df
               ,paste0(Sys.Date()
                       ,"_toxdb_biopax_summary_analysis--"
                       ,label
                       ,"--genes.xlsx")
               ,col.names = TRUE
               ,row.names = FALSE)    
    
    return(summary_df)
    
  }