R/create_kegg_map.R

In w-korani/keggseq: KEGG analysis and visualizing of differentially expressed genes

#'name create_kegg_map
create_kegg_map <- function (species,dataset,deg_list,map_number,
    correction_file_name)
{
    a1 = formatC(map_number,width = 5, format = "d",flag="0")
    a2 = paste0("http://www.kegg.jp/kegg-bin/show_pathway?map",
    a1,"/")
    b1 = dataset[dataset$map_numbers==a1,6]
    b2 = strsplit(b1,", ")
    b3 = as.matrix(b2[[1]])
    b4 = gsub(',','',b3)
    b5 = intersect(as.matrix(deg_list),b4)
    Table5 = data.frame()
    for (i in 1:length(species))
    {
    link1 = "http://rest.kegg.jp/link/"
    Link1 = paste0(link1,species[i],"/enzyme")
    Table1 = readLines(Link1)
    Table2 = t(data.frame(strsplit(Table1,'\t')))
    Table3 = cbind(kegg_enzymes = as.character(Table2[,1]),
    kegg_genes = as.character(Table2[,2]))
    Table5 = rbind(Table5,Table3)
    }
    kegg_enzymes = as.matrix(unique(Table5[,1]))
    uniq_list = as.data.frame(Table5[,1])
    colnames(uniq_list) = c("list")
    uniq_list = as.data.frame(uniq_list[order(uniq_list$list),])
    dup=duplicated(uniq_list)
    uniq_list = as.matrix(uniq_list[dup,])
    uniq_list = setdiff(kegg_enzymes,uniq_list)
    not_uniq_list = setdiff(kegg_enzymes,uniq_list)
    if (missing(correction_file_name))
    {
    Table6 = Table5[Table5$kegg_genes %in% b5,]#==
    }
    else
    {
    cc = read.csv(correction_file_name,header=FALSE)
    colnames(cc) = c('new','kegg_genes')
    Table5b = merge(Table5,cc,by = 'kegg_genes')
    Table5 = Table5b[,2:3]
    colnames(Table5)[2] = "kegg_genes"
    Table6 = data.frame()
    for (x in 1:length(b5))
    {
    Table6 = rbind(Table6,Table5[as.character(Table5$kegg_genes) == b5[x],])
    }
    }
    a3 = ""
    for (i in 1:dim(Table6)[1])
    {
    if (length(uniq_list[uniq_list == Table6$kegg_enzymes[i]]) > 0)
    {
    a3 = paste0(a3,gsub('\\w*:','',as.character(Table6$kegg_enzymes[i]))
    ,"%09yellow/")
    }
    if (length(not_uniq_list[not_uniq_list == Table6$kegg_enzymes[i]]) > 0)
    {
    a3 = paste0(a3,gsub('\\w*:','',as.character(Table6$kegg_enzymes[i])),
    "%09grey/")
    }
    }
    a4 = paste0(a2,a3)
    a5 = readLines(a4)
    a6 = a5[grep(".*?value=/share/www/mark_pathway.*?/map*",a5)]
    a7 = sub(".*?value=/share/www/mark_pathway(.*?)/map.*?.png>","\\1",a6)
    a8 = paste0("http://www.kegg.jp/tmp/mark_pathway",a7,"/map",a1,".png")
    download.file(a8,destfile=paste0(a1,".png"),mode ='wb')
    browseURL(a4)
    write.table(Table5,paste0(a1,"_enzymes.csv"),row.names = FALSE,sep=",")
    write.table(Table6,paste0(a1,"_de_enzymes.csv"),row.names = FALSE,sep=",")
}