R/kegg2DT.R

In fpsanz/enrichGene:

kegg2DT <- function(enrichdf, data, orderby = NULL, nrows = NULL) {
    if(!is.data.frame(enrichdf) | !is.data.frame(data)){
        stop("enrichdf and data should be data.frame")
    }
    names(data) <- c("SYMBOL", "ENTREZID")
    if(!is.null(orderby)){
        orderby = match.arg(orderby, c("DE", "P.DE", "N", "Pathway"))
        if(orderby=="P.DE" | orderby =="Pathway"){
            enrichdf <- enrichdf %>% arrange(get(orderby))
        } else{ enrichdf <- enrichdf %>% arrange(desc(get(orderby)))}
    }
    enrichdf2 <- enrichdf %>%
        mutate(pathway = limma::strsplit2(enrichdf$pathID, ":")[, 2],
               genesURL = gsub(",", "+", genes)) %>%
        mutate(url = paste0("<a href='https://www.kegg.jp/kegg-bin/show_pathway?",
        pathway, "/", genesURL, "'>", pathway, "</a>"))
    CAup <- enrichdf2[, c(1, 2, 3, 4, 6, 9)]
    CAup$genes <- gsub(",", ", ", CAup$genes)
    for (i in seq(1:length(CAup$genes))) {
        mg <- as.numeric(unlist(strsplit(CAup$genes[i], ", ")))
        mg2 <- match(mg, data$ENTREZID)
        CAup$genes[i] <- paste0(data[mg2, 1], collapse = ", ")
    }
    splitGenes <- strsplit(CAup$genes, ", ")
    CAup$genes <- lapply(
        splitGenes, function(x){
            paste(sort(x), collapse = ", ")
            }
        )
    if(!is.null(nrows) & is.numeric(nrows)){
        CAup <- CAup[1:nrows, ]
    }
    CAup <- CAup %>% mutate(P.DE = format(P.DE, scientific = T, digits = 4))
    return(CAup)
}