R/keggAnno.R

In jmzeng1314/humanid: gene id annotation

#' annotate KEGG pathway for entrez id or symbol
#'
#' somethins
#'
#' @param geneLists a character vector for gene entrez ID list,default: c(1,2,9)
#' @param fileType     choose whether annotate gene name     for the gene id or not , default : T
#' @param fileName      choose whether annotate gene map      for the gene id or not , default : F
#' @param multiple  choose whether annotate gene ensembl  for the gene id or not , default : F
#' @return write a html or csv files for the annotation results.
#' @export
#' @keywords keggAnno
#' @examples
#' #' keggAnno('TP53',fileName='TP53',multiple = F),keggAnno('TP53')



keggAnno <- function(geneLists = c(1, 2, 9), fileType = "html", fileName = "gene", multiple = T) {
    results <- geneAnno(geneLists)
    tmp = merge(results, keggID2geneID_df, by = "gene_id", all.x = T)
    keggID2name = kegg2name[, 3:4]
    colnames(keggID2name) = c("path_id", "path_name")
    tmp2 = merge(tmp, keggID2name, by = "path_id", all.x = T)
    kegg_info = tmp2
    ## 5 columns: path_id,gene_id,symbol,gene_name,path_name we need to add links for the path according to the
    ## path_id and path_name !!
    
    if (fileType != "html") {
        write.csv(kegg_info, paste0(fileName, "_kegg_anno.csv"), row.names = F)
    } else {
        if (multiple) {
            kegg_info$pathway_name = apply(kegg_info, 1, function(x) {
                ## create a new column for kegg_info !!! path_id gene_id symbol path_name
                tmp = ""
                if (is.na(x["path_id"])) {
                  tmp = "NA"
                } else {
                  
                  pathwayID = sprintf("%05.0f", as.numeric(x["path_id"]))
                  pathwayName = x["path_name"]
                  href = paste0("http://www.genome.jp/kegg-bin/show_pathway?hsa", pathwayID, "+hsa:", x["gene_id"])
                  tmp = paste0("<b><a target=\"_black\" href=", shQuote(href), ">", pathwayName, "</a></b>")
                  
                }
                return(tmp)
            })  ## we add the links in the new column: pathway_name
            new_kegg_info = kegg_info[order(kegg_info[, "gene_id"]), ]
        } else {
            new_kegg_info <- data.frame(matrix(unlist(lapply(split(kegg_info, kegg_info$gene_id), function(gene_id_kegg_info) {
                gene_id_kegg_info$pathway_name <- apply(gene_id_kegg_info, 1, function(x) {
                  tmp = ""
                  if (is.na(x["path_id"])) {
                    tmp = "NA"
                  } else {
                    
                    pathwayID = sprintf("%05.0f", as.numeric(x["path_id"]))
                    pathwayName = x["path_name"]
                    href = paste0("http://www.genome.jp/kegg-bin/show_pathway?hsa", pathwayID, "+hsa:", x["gene_id"])
                    tmp = paste0("<b><a target=\"_black\" href=", shQuote(href), ">", pathwayName, "</a></b>")
                    
                  }
                  return(tmp)
                })  ## end for apply
                links = paste(gene_id_kegg_info$pathway_name, collapse = ",")
                return(c(gene_id_kegg_info[1, c("gene_id", "symbol", "gene_name")], links))
            })  ## end for lapply +split
)  ## end for unlist
, ncol = 4, 
                byrow = T)  ## end for matrix
, stringsAsFactors = FALSE)  ## endor data.frame
            colnames(new_kegg_info) = c("gene_id", "symbol", "gene_name", "kegg_links")
        }
        y <- DT::datatable(new_kegg_info, escape = F, rownames = F)
        DT::saveWidget(y, paste0(fileName, "_kegg_anno.html"))
    }
    
}