R/interactions_df_to_biopax_dt.R

In grishagin/RIGconvertbiopax: Convert BioPAX into Flat File and Back

######################################## interactions_df_to_biopax_dt ########################################
interactions_df_to_biopax_dt<-
    function(interactions_df){
        
        #' @title
        #' Convert Interactions Dataframe into BioPAX Data Table
        #' @description 
        #' Convert dataframe of interactions into a BioPAX-style data table. 
        #' @details 
        #' Takes in a dataframe returned by \code{MAIN_flatten_biopax}, 
        #' and parses each value to return a BioPAX-style data table.
        #' @param interactions_df \code{MAIN_flatten_biopax} output dataframe.
        
        #' @author 
        #' Ivan Grishagin
        
        st<-Sys.time()
        message("Converting a dataframe with interactions into a biopax data table...")
        
        #prepare auxiliary dataframe with pw names, ids, etc.
        aux_df<-
            interactions_df %>%
            internal_make_main_aux_df
        
        #prepare interactions_df for processing and extraction of components
        interactions_df_list<-
            list() 
        #evidence...
        interactions_df_list$evidence<-
            interactions_df %>%
            .[,grep("pathwayComponent"
                    ,colnames(.))]
        
        #... controllers...
        interactions_df_list$controller<-
            interactions_df %>%
            filter(!is.na(controller_id)) %>%
            .[,grep("controller_"
                    ,colnames(.))] 
        
        #... controlled...
        interactions_df_list$controlled<-
            interactions_df %>% 
            filter(!is.na(controlled_id)) %>%
            .[,grep("controlled_"
                    ,colnames(.))] 
        
        #... and other non-control components 
        interactions_df_list$noncontrol<-
            interactions_df %>%
            filter(!is.na(noncontrol_id)) %>%
            .[,grep("noncontrol_"
                    ,colnames(.))] 
        
        #strip column name identifiers to make them uniform regardless of exact case
        for(index in 1:length(interactions_df_list)){
            colnames(interactions_df_list[[index]])<-
                colnames(interactions_df_list[[index]]) %>%
                gsub("controller_|controlled_|noncontrol_|pathwayComponent_"
                     ,""
                     ,.)
        }
        
        #get dt of all components
        comp_df<-
            lapply(interactions_df_list
                   ,internal_indf_list_element_to_biopax_dt) %>%
            do.call(rbind.data.frame
                    ,.) 
        
        #assemble the final dt
        dTable<-
            rbind.data.frame(aux_df
                             ,comp_df)
        
        #remove duplicates
        #remove rows with NA values
        #replace placeholder classes
        dTable<-
            dTable %>%
            unique %>%
            .[complete.cases(.),] %>% 
            #replace PLACEHOLDERs 
            #with corresponding classes and properties
            internal_fix_placeholders %>% 
            as.data.table
        
        et<-Sys.time()
        
        msg<-
            paste0("Conversion of a flat file with interactions took "
                   ,round(difftime(et
                                   ,st
                                   ,units = "mins")
                          ,1)
                   ," minutes.")
        message(msg)
        write(msg
              ,"time_log.txt"
              ,sep = "\n"
              ,append=TRUE)
        
        return(dTable)
    }
######################################## interactions_df_to_biopax_dt ########################################

#' ######################################## interactions_df_to_biopax_dt ########################################
#' interactions_df_to_biopax_dt<-
#'     function(interactions_df){
#'         
#'         #' @title
#'         #' Convert Interactions Dataframe into BioPAX Data Table
#'         #' @description 
#'         #' Convert dataframe of interactions into a BioPAX-style data table. 
#'         #' @details 
#'         #' Takes in a dataframe returned by \code{MAIN_flatten_biopax}, 
#'         #' and parses each value to return a BioPAX-style data table.
#'         #' @param interactions_df \code{MAIN_flatten_biopax} output dataframe.
#'         
#'         #' @author 
#'         #' Ivan Grishagin
#'             
#'         st<-Sys.time()
#'         message("Converting a dataframe with interactions into a biopax data table...")
#'         
#'         #prepare auxiliary dataframe with pw names, ids, etc.
#'         aux_df<-
#'             interactions_df %>%
#'             internal_make_main_aux_df
#'         
#'         #prepare interactions_df for processing and extraction of components
#'         interactions_df_list<-
#'             list() 
#'         #controllers...
#'         interactions_df_list$controller<-
#'             interactions_df %>%
#'             filter(!is.na(controller_id)) %>%
#'             .[,grep("controller_"
#'                     ,colnames(.))] 
#'         
#'         #... controlled...
#'         interactions_df_list$controlled<-
#'             interactions_df %>% 
#'             filter(!is.na(controlled_id)) %>%
#'             .[,grep("controlled_"
#'                     ,colnames(.))] 
#' 
#'         #... and other non-control components 
#'         #ATTENTION: non_ctrl_component column must be logical
#'         if (class(interactions_df$non_ctrl_component)!="logical"){
#'             interactions_df$non_ctrl_component<-
#'                 as.logical(interactions_df$non_ctrl_component)
#'         }
#'         interactions_df_list$non_ctrl_component<-
#'             interactions_df %>%
#'             filter(non_ctrl_component) %>%
#'             .[,grep("non_ctrl_component_|^component_"
#'                     ,colnames(.))] 
#'         
#'         #strip column name identifiers to make them uniform regardless of exact case
#'         for(index in 1:length(interactions_df_list)){
#'             colnames(interactions_df_list[[index]])<-
#'                 colnames(interactions_df_list[[index]]) %>%
#'                 gsub("controller_|controlled_|non_ctrl_component_|component_"
#'                      ,""
#'                      ,.) %>%
#'                 gsub("complex"
#'                      ,"component_"
#'                      ,.)
#'         }
#'         
#'         #get dt of all components
#'         comp_df<-
#'             lapply(interactions_df_list
#'                    ,internal_indf_list_element_to_biopax_dt) %>%
#'             do.call(rbind.data.frame
#'                     ,.) 
#'         
#'         #assemble the final dt
#'         dTable<-
#'             rbind.data.frame(aux_df
#'                              ,comp_df)
#'         
#'         #remove duplicates
#'         #remove rows with NA values
#'         #replace placeholder classes
#'         dTable<-
#'             dTable %>%
#'             unique %>%
#'             .[complete.cases(.),] %>% 
#'             #replace PLACEHOLDERs 
#'             #with corresponding classes and properties
#'             internal_fix_placeholders
#'        
#' 
#'         et<-Sys.time()
#'         
#'         msg<-
#'             paste0("Conversion of a flat file with interactions took "
#'                    ,round(difftime(et
#'                                    ,st
#'                                    ,units = "mins")
#'                           ,1)
#'                    ," minutes.")
#'         message(msg)
#'         write(msg
#'               ,"time_log.txt"
#'               ,sep = "\n"
#'               ,append=TRUE)
#'         
#'         return(dTable)
#'     }
#' ######################################## interactions_df_to_biopax_dt ########################################