R/add_edge_data.R

In KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

#' Annotate KEGG edge mappings with user data
#' @description Add data column[s] to object created from function 
#' expand_KEGG_edges 
#' @export
#' @importFrom gtools smartbind
#' @importFrom plyr rename
#' @param expanded_edges The data frame object generated via the function 
#' expand_KEGG_edges  
#' @param KEGG_mappings KEGG_mappings The data.frame object generated by the 
#' function expand_KEGG_mappings
#' @param user_data A data frame where in which the first two columns contain 
#' gene symbols representing an edge and any/all other column[s] contain 
#' corresponding edge data.
#' @param data_column_no The column index for desired user data to be added
#' @param map_type If the genes in your data set are left untranslated 
#' set to "NUMBER" (assuming numbers are gene accession numbers) 
#' @param only_mapped A logical indicator; if set to FALSE will return 'de-novo'
#' edges that 'exist' in data but are not documented in KEGG 
#' @return A data frame object with detailed KEGG edge mappings annotated with 
#' user data
#' @examples 
#' p53_KGML <- get_KGML('hsa04115')
#' p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)
#' p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
#' p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 'HA1E', 
#'                                data_type = '100_bing', only_mapped = FALSE)
#'                                
#' p53_edges_HA1E <- add_edge_data(p53_edges, p53_KEGG_mappings, 
#'                                         p53_HA1E_data, c(3, 10,12))


add_edge_data <- function(expanded_edges, KEGG_mappings,
                          user_data, data_column_no = 3, map_type = "SYMBOL",
                          only_mapped = TRUE) {
    
    expanded_edges <- expanded_edges[expanded_edges$type != "maplink", ]
    if (nrow(expanded_edges) > 0) {
        if (map_type == "SYMBOL"){
            expanded_edges$unique_ID = 
                paste0(expanded_edges$entry1symbol, ",",
                expanded_edges$entry2symbol)
            expanded_edges$unique_IDR = 
                paste0(expanded_edges$entry2symbol, ",",
                expanded_edges$entry1symbol)
        }
        if (map_type == "NUMBER"){
            expanded_edges$unique_ID = 
                paste0(expanded_edges$entry1accession, ",",
                expanded_edges$entry2accession)
            expanded_edges$unique_IDR = 
                paste0(expanded_edges$entry2accession, ",",
                expanded_edges$entry1accession)
        }
        
        user_data$unique_ID = paste0(user_data[,1], ",",
                                     user_data[,2])
        pre_mapped1 <- subset(user_data, user_data$unique_ID %in%
                                  expanded_edges$unique_ID)
        pre_mapped2 <- subset(user_data, user_data$unique_ID %in%
                                  expanded_edges$unique_IDR)
        pre_mapped2 <- pre_mapped2[, c(2, 1, 3:ncol(pre_mapped2))]
        names(pre_mapped2) = names(pre_mapped1)
        if (nrow(pre_mapped2) >= 1 & nrow(pre_mapped1) >= 1) {
            pre_mapped2$unique_ID <- paste0(pre_mapped2[,1], ",",
                                            pre_mapped2[,2])
            pre_mapped <- rbind(pre_mapped1, pre_mapped2)
        }
        if (nrow(pre_mapped2) == 0 & (nrow(pre_mapped1) == 0)) {
            pre_mapped <- data.frame(unique_ID = NA)
        }
        if (nrow(pre_mapped1) == 0 & nrow(pre_mapped2) >= 1) {
            pre_mapped2$unique_ID <- paste0(pre_mapped2[,1], ",",
                                            pre_mapped2[,2])
            pre_mapped <- pre_mapped2
        }
        if (nrow(pre_mapped2) == 0 & nrow(pre_mapped1) >= 1) {
            pre_mapped <- pre_mapped1
        }
        if (!is.na(pre_mapped[1, 1])) {
            expanded_edges_1 <- subset(expanded_edges, expanded_edges$unique_ID
                                       %in% pre_mapped$unique_ID)
            expanded_edges_1 <- expanded_edges[expanded_edges$unique_ID %in%
                                                   pre_mapped$unique_ID, ]
            expanded_edges_2 <- expanded_edges[!expanded_edges$unique_ID %in%
                                                   pre_mapped$unique_ID, ]
            expanded_edges_1$has_data = 1
            testval <- nrow(expanded_edges_2)
            if (testval > 0) {
                expanded_edges_2$has_data = 0
                edge_set <- rbind(expanded_edges_1, expanded_edges_2)
            }
            else {
                edge_set <- expanded_edges_1
            }
            
            edge_set <- edge_set[order(edge_set$unique_ID), ]
            
            data_to_add <- data.frame("unique_ID" = pre_mapped$unique_ID, stringsAsFactors = FALSE)
            data_to_add <- cbind(data_to_add, pre_mapped[, data_column_no])
            
            data_to_add <- data_to_add[order(data_to_add$unique_ID), ]
            colnames(data_to_add)[2] <- "summary_score"
            
            annotated_edges <- merge(edge_set, data_to_add, "unique_ID",
                                     all.x = TRUE)
            drops <- c("unique_ID", "unique_IDR")
            annotated_edges <- annotated_edges[, !(names(annotated_edges) %in%
                                                       drops)]
            cat(paste0("Number of edges documented in selected pathway = ",
                       nrow(annotated_edges)), "\n")
            cat(paste0("Number of edges with corresponding user data = ",
                       sum(annotated_edges$has_data), "\n"))
            cat(paste0("Coverage = ", round(sum(annotated_edges$has_data)/
                                                nrow(annotated_edges) * 100, 2), "%", "\n"))
            annotated_edges$premapped <- 1
            # un_mapped <- subset(user_data, !user_data$unique_ID %in%
            #                       expanded_edges$unique_ID &
            #                       !user_data$unique_ID %in% expanded_edges$unique_IDR)
            # un_mapped_edges <- un_mapped[, c(1:2, data_column_no,
            #                                  ncol(un_mapped))]
            
            if (only_mapped) {
                return(annotated_edges)
            }
        }
        else {
            annotated_edges <- expanded_edges
            annotated_edges$premapped <- 1
            annotated_edges$has_data <- 0
            un_mapped <- user_data
            un_mapped$unique_ID <- paste0(un_mapped$knockout1,
                                          un_mapped$knockout2)
            un_mapped_edges <- un_mapped[, c(1:2, data_column_no,
                                             ncol(un_mapped))]
            un_mapped_edges$premapped <- 0
            un_mapped_edges$has_data <- 0
            cat(paste0("Number of edges documented in selected pathway = ",
                       nrow(annotated_edges)), "\n")
            cat(paste0("Number of edges with corresponding user data = ",
                       sum(annotated_edges$has_data), "\n"))
            cat(paste0("Coverage = ", round(sum(annotated_edges$has_data)/
                                                nrow(annotated_edges) * 100, 2), "%", "\n"))
            if (only_mapped) {
                cat(paste0("No documented edges are found in data;
                           only data for de-novo edges can be mapped \n"))
                return(annotated_edges)
            }
        }
        }
    else if (nrow(expanded_edges) == 0) {
        annotated_edges <- expanded_edges
        annotated_edges$premapped <- 1
        annotated_edges$has_data <- 0
        un_mapped <- user_data
        un_mapped$unique_ID <- paste0(un_mapped$knockout1, un_mapped$knockout2)
        un_mapped_edges <- un_mapped[, c(1:2, data_column_no, ncol(un_mapped))]
        un_mapped_edges$premapped <- 0
        un_mapped_edges$has_data <- 0
        cat(paste0("Number of edges documented in selected pathway = ",
                   nrow(annotated_edges)), "\n")
        cat(paste0("Number of edges with corresponding user data = ",
                   sum(annotated_edges$has_data), "\n"))
        cat(paste0("Coverage = ", round(sum(annotated_edges$has_data)/
                                            nrow(annotated_edges) * 100, 2), "%", "\n"))
        if (only_mapped) {
            return(annotated_edges)
        }
    }
    names(un_mapped_edges)[1:2] <- c("entryNAME_1", "entryNAME_2")
    for (i in 1:nrow(un_mapped_edges)) {
        un_mapped_edges$Source_eid[i] <-
            list(KEGG_mappings$entryID[which(KEGG_mappings$entrySYMBOL ==
                                                 un_mapped_edges$entryNAME_1[i])])
        un_mapped_edges$Target_eid[i] <-
            list(KEGG_mappings$entryID[which(KEGG_mappings$entrySYMBOL ==
                                                 un_mapped_edges$entryNAME_2[i])])
        x <- length(unlist(un_mapped_edges$Source_eid[i]))
        y <- length(unlist(un_mapped_edges$Target_eid[i]))
        if (x > 1 | y > 1) {
            un_mapped_edges$simple[i] <- FALSE
        } else {
            un_mapped_edges$simple[i] <- TRUE
        }
    }
    simple_un_mapped_edges <- un_mapped_edges[un_mapped_edges$simple == TRUE,
                                              -ncol(un_mapped_edges)]
    complex_un_mapped_edges <- un_mapped_edges[un_mapped_edges$simple == FALSE,
                                               -ncol(un_mapped_edges)]
    test_val <- nrow(complex_un_mapped_edges)
    if (test_val == 0) {
        un_mapped_edges <- simple_un_mapped_edges
    } else {
        keeps <- c("Source_eid", "Target_eid", "unique_ID")
        c_temp <- complex_un_mapped_edges[, (names(complex_un_mapped_edges) %in%
                                                 keeps)]
        
        for (i in 1:nrow(c_temp)) {
            x <- length(unlist(c_temp$Source_eid[i]))
            y <- length(unlist(c_temp$Target_eid[i]))
            l <- x * y
            
            c_temp$Source_eid[i] <- list(sort(unlist(rep(c_temp$Source_eid[i],
                                                         y))))
            c_temp$Target_eid[i] <- list(unlist(rep(c_temp$Target_eid[i], x)))
            c_temp$unique_ID[i] <- list(rep(c_temp$unique_ID[i], l))
        }
        
        c_temp <- data.frame(unique_ID = unlist(c_temp$unique_ID), Source_eid =
                                 unlist(c_temp$Source_eid),
                             Target_eid = unlist(c_temp$Target_eid))
        drops <- c("Source_eid", "Target_eid")
        complex_un_mapped_edges <-
            complex_un_mapped_edges[, !(names(complex_un_mapped_edges) %in%
                                            drops)]
        complex_un_mapped_edges <- merge(complex_un_mapped_edges, c_temp)
        un_mapped_edges <- rbind(simple_un_mapped_edges,
                                 complex_un_mapped_edges)
    }
    un_mapped_edges$Source_eid <- unlist(un_mapped_edges$Source_eid)
    un_mapped_edges$Target_eid <- unlist(un_mapped_edges$Target_eid)
    un_mapped_edges <- plyr::rename(un_mapped_edges, c(Source_eid = "entry1",
                                                       Target_eid = "entry2", entryNAME_1 = "entry1symbol",
                                                       entryNAME_2 = "entry2symbol"))
    un_mapped_edges$subtype1 <- "de_novo"
    
    drops <- c("unique_ID")
    un_mapped_edges <- un_mapped_edges[, !(names(un_mapped_edges) %in% drops)]
    un_mapped_edges$has_data <- 1
    un_mapped_edges$premapped <- 0
    for (i in 1:nrow(un_mapped_edges)) {
        un_mapped_edges$entry1accession[i] <-
            KEGG_mappings$entryACCESSION[which(KEGG_mappings$entrySYMBOL ==
                                                   un_mapped_edges$entry1symbol[i])][1]
        un_mapped_edges$entry2accession[i] <-
            KEGG_mappings$entryACCESSION[which(KEGG_mappings$entrySYMBOL ==
                                                   un_mapped_edges$entry2symbol[i])][1]
        un_mapped_edges$entry1type[i] <-
            KEGG_mappings$entryTYPE[which(KEGG_mappings$entrySYMBOL ==
                                              un_mapped_edges$entry1symbol[i])][1]
        un_mapped_edges$entry2type[i] <-
            KEGG_mappings$entryTYPE[which(KEGG_mappings$entrySYMBOL ==
                                              un_mapped_edges$entry2symbol[i])][1]
    }
    
    if (nrow(annotated_edges) > 0 & nrow(un_mapped_edges) > 0) {
        all_edges <- gtools::smartbind(annotated_edges, un_mapped_edges)
    } else if (nrow(annotated_edges) > 0)
        all_edges <- annotated_edges else {
            all_edges <- un_mapped_edges
            all_edges$value <- NA
            all_edges$subtype2 <- NA
            all_edges$value2 <- NA
            all_edges$specific_subtype <- NA
            all_edges$type <- NA
            all_edges$is_direct <- 1
            all_edges$edgeID <- seq(1:nrow(un_mapped_edges))
            refcols <- c("edgeID", "entry1accession", "entry2accession", "entry1",
                         "entry2")
            all_edges <- all_edges[, c(refcols, setdiff(names(all_edges), refcols))]
            cat(paste0("All documented edges are of type maplink; only data for
                       de-novo edges can be mapped \n"))
        }
    
    for (i in 1:nrow(all_edges)) {
        if (all_edges$entry1[i] == all_edges$entry2[i]) {
            all_edges$paralogs[i] <- 1
        } else {
            all_edges$paralogs[i] <- 0
        }
    }
    return(all_edges)
        }