--- a/kegg_maps_visualization.R	Thu Mar 05 13:45:08 2020 +0000
+++ b/kegg_maps_visualization.R	Mon May 10 12:45:44 2021 +0000
@@ -1,366 +1,427 @@
 #!/usr/bin/Rscript
 #Rscript made for mapping genesID on KEGG pathway with Pathview package
-#input : csv file containing ids (uniprot or geneID) to map, plus parameters
+#input : csv file containing ids (uniprot or geneid) to map, plus parameters
 #output : KEGG pathway : jpeg or pdf file.
 
-options(warn=-1)  #TURN OFF WARNINGS !!!!!!
+options(warn = -1)  #TURN OFF WARNINGS !!!!!!
 suppressMessages(library("pathview"))
 suppressMessages(library(KEGGREST))
 
-read_file <- function(path,header){
-    file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F, comment.char = ""),silent=TRUE)
-    if (inherits(file,"try-error")){
-      stop("Read file error ! Please check your file (header, # character, etc) ")
-    }else{
+read_file <- function(path, header) {
+    file <- try(read.csv(path, header = header, sep = "\t",
+            stringsAsFactors = FALSE, quote = "\"", check.names = F,
+            comment.char = ""), silent = TRUE)
+    if (inherits(file, "try-error")) {
+      stop("Read file error! Please check your file (header, # character, etc)")
+    }else {
       return(file)
     }
 }
 
-##### fuction to clean and concatenate pathway name (allow more flexibility for user input) 
-concat_string <- function(x){
-  x <- gsub(" - .*","",x)
-  x <- gsub(" ","",x)
-  x <- gsub("-","",x)
-  x <- gsub("_","",x)
-  x <- gsub(",","",x)
-  x <- gsub("\\'","",x)
-  x <- gsub("\\(.*)","",x)
-  x <- gsub("\\/","",x)
+##### fuction to clean and concatenate pathway name
+##### (allow more flexibility for user input)
+concat_string <- function(x) {
+  x <- gsub(" - .*", "", x)
+  x <- gsub(" ", "", x)
+  x <- gsub("-", "", x)
+  x <- gsub("_", "", x)
+  x <- gsub(",", "", x)
+  x <- gsub("\\'", "", x)
+  x <- gsub("\\(.*)", "", x)
+  x <- gsub("\\/", "", x)
   x <- tolower(x)
   return(x)
 }
 
 #return output suffix (pathway name) from id kegg (ex : hsa:00010)
-get_suffix <- function(pathways_list,species,id){
-  suffix = gsub("/","or",pathways_list[pathways_list[,1]==paste(species,id,sep=""),2])
-  suffix = gsub(" ","_",suffix)
-  if (nchar(suffix) > 50){
-    suffix = substr(suffix,1,50)
+get_suffix <- function(pathways_list, species, id) {
+  suffix <- gsub("/", "or", pathways_list[pathways_list[, 1] == paste(
+    species, id, sep = ""), 2])
+  suffix <- gsub(" ", "_", suffix)
+  if (nchar(suffix) > 50) {
+    suffix <- substr(suffix, 1, 50)
   }
   return(suffix)
 }
 
-str2bool <- function(x){
-  if (any(is.element(c("t","true"),tolower(x)))){
-    return (TRUE)
-  }else if (any(is.element(c("f","false"),tolower(x)))){
-    return (FALSE)
-  }else{
+str2bool <- function(x) {
+  if (any(is.element(c("t", "true"), tolower(x)))) {
+    return(TRUE)
+  }else if (any(is.element(c("f", "false"), tolower(x)))) {
+    return(FALSE)
+  }else {
     return(NULL)
   }
 }
 
-is.letter <- function(x) grepl("[[:alpha:]]", x)
+is_letter <- function(x) grepl("[[:alpha:]]", x)
 
-#### hsa00010 -> 00010
-remove_kegg_prefix <- function(x){
-  x = gsub(":","",x)
-  if (substr(x,1,4) == 'path'){
-    x=substr(x,5,nchar(x))
+remove_kegg_prefix <- function(x) {
+  x <- gsub(":", "", x)
+  if (substr(x, 1, 4) == "path") {
+    x <- substr(x, 5, nchar(x))
   }
-  if (is.letter(substr(x,1,3))){
-    x <- substr(x,4,nchar(x))
+  if (is_letter(substr(x, 1, 3))) {
+    x <- substr(x, 4, nchar(x))
   }
   return(x)
 }
 
-kegg_to_geneID <- function(vector){
-  vector <- sapply(vector, function(x) unlist(strsplit(x,":"))[2],USE.NAMES = F)
-  return (vector)
+kegg_to_geneid <- function(vector) {
+  #nolint start
+  vector <- sapply(vector, function(x) unlist(
+    strsplit(x, ":"))[2], USE.NAMES = F)
+  #nolint end
+  return(vector)
 }
 
 clean_bad_character <- function(string)  {
-  string <- gsub("X","",string)
+  string <- gsub("X", "", string)
   return(string)
 }
 
-get_list_from_cp <-function(list){
-  list = gsub(";","\t",list)
-  list = gsub(",","\t",list)
-  list = strsplit(list, "[ \t\n]+")[[1]]
-  list = list[list != ""]    #remove empty entry
-  list = gsub("-.+", "", list)  #Remove isoform accession number (e.g. "-2")
+get_list_from_cp <- function(list) {
+  list <- gsub(";", "\t", list)
+  list <- gsub(",", "\t", list)
+  list <- strsplit(list, "[ \t\n]+")[[1]]
+  list <- list[list != ""]    #remove empty entry
+  list <- gsub("-.+", "", list)  #Remove isoform accession number (e.g. "-2")
   return(list)
 }
 
-get_ref_pathways <- function(species){
+get_ref_pathways <- function(species) {
   ##all available pathways for the species
   pathways <- keggLink("pathway", species)
   tot_path <- unique(pathways)
-  
+
   ##formating the dat into a list object
   ##key= pathway ID, value = genes of the pathway in the kegg format
-  pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway)))
-  return (pathways_list)
+  pathways_list <- sapply(tot_path, function(pathway)
+    names(which(pathways == pathway)))
+  return(pathways_list)
 }
 
-mapping_summary <- function(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID){
-  ref_pathways = get_ref_pathways(species)
-  names(ref_pathways) <- sapply(names(ref_pathways), function(x) gsub("path:[a-z]{3}","",x),USE.NAMES = F)
-  
+#nolint start
+mapping_summary <- function(pv_out, species, id, id_type, pathways_list,
+                            geneid, uniprotid, mapped2geneid) {
+  ref_pathways <- get_ref_pathways(species)
+  names(ref_pathways) <- sapply(names(ref_pathways), function(x)
+        gsub("path:[a-z]{3}", "", x), USE.NAMES = F)
+#nolint end
   #genes present in pathway
-  genes = ref_pathways[id][[1]]
-  nb_genes = length(genes)
-  
+  genes <- ref_pathways[id][[1]]
+  nb_genes <- length(genes)
+
   #genes mapped on pathway genes
-  mapped <- unlist(sapply(pv.out$plot.data.gene$all.mapped, function(x) strsplit(x,",")),use.names = F)
-  mapped = unique(mapped[mapped!=""])
+  mapped <- unlist(sapply(pv_out$plot.data.gene$all.mapped,
+                          function(x) strsplit(x, ",")), use.names = F)
+  mapped <- unique(mapped[mapped != ""])
   nb_mapped <- length(mapped)
-  
-  #compue ratio of mapping
-  ratio = round((nb_mapped/nb_genes)*100, 2)
-  if (is.nan(ratio)) { ratio = ""}
-  pathway_id = paste(species,id,sep="")
-  pathway_name = as.character(pathways_list[pathways_list[,1]==pathway_id,][2])
-  
-  if (id_type=="geneid" || id_type=="keggid") {
-    row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_mapped,nb_genes,ratio,paste(mapped,collapse=";"))
-    names(row) <- c("KEGG pathway ID","pathway name","nb of Entrez gene ID used","nb of Entrez gene ID mapped",
-                    "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped")
-  } else if (id_type=="uniprotid") {
-    row <- c(pathway_id,pathway_name,length(unique(uniprotID)),length(unique(geneID)),nb_mapped,nb_genes,ratio,paste(mapped,collapse=";"),paste(mapped2geneID[which(mapped2geneID[,2] %in% mapped)],collapse=";"))
-    names(row) <- c("KEGG pathway ID","pathway name","nb of Uniprot_AC used","nb of Entrez gene ID used","nb of Entrez gene ID mapped",
-                    "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped","uniprot_AC mapped")
-  } 
+
+  #compute ratio of mapping
+  ratio <- round((nb_mapped / nb_genes) * 100, 2)
+  if (is.nan(ratio)) {
+    ratio <- ""
+    }
+  pathway_id <- paste(species, id, sep = "")
+  pathway_name <- as.character(
+    pathways_list[pathways_list[, 1] == pathway_id, ][2])
+
+  if (id_type == "geneid" || id_type == "keggid") {
+    row <- c(pathway_id, pathway_name, length(unique(geneid)),
+             nb_mapped, nb_genes, ratio, paste(mapped, collapse = ";"))
+    names(row) <- c("KEGG pathway ID", "pathway name",
+                    "nb of Entrez gene ID used", "nb of Entrez gene ID mapped",
+                    "nb of Entrez gene ID in the pathway",
+                    "ratio of Entrez gene ID mapped (%)",
+                    "Entrez gene ID mapped")
+  } else if (id_type == "uniprotid") {
+    row <- c(pathway_id, pathway_name, length(unique(uniprotid)),
+             length(unique(geneid)), nb_mapped, nb_genes, ratio,
+             paste(mapped, collapse = ";"),
+             paste(mapped2geneid[which(mapped2geneid[, 2] %in% mapped)],
+                   collapse = ";"))
+    names(row) <- c("KEGG pathway ID", "pathway name", "nb of Uniprot_AC used",
+                    "nb of Entrez gene ID used", "nb of Entrez gene ID mapped",
+                    "nb of Entrez gene ID in the pathway",
+                    "ratio of Entrez gene ID mapped (%)",
+                    "Entrez gene ID mapped", "uniprot_AC mapped")
+  }
   return(row)
 }
 
 #take data frame, return  data frame
-split_ids_per_line <- function(line,ncol){
-  
+split_ids_per_line <- function(line, ncol) {
+
   #print (line)
-  header = colnames(line)
-  line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol])
-  
-  if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
-    if (length(line)==1 ) {
-      lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
+  header <- colnames(line)
+  line[ncol] <- gsub("[[:blank:]]|\u00A0", "", line[ncol])
+
+  if (length(unlist(strsplit(as.character(line[ncol]), ";"))) > 1) {
+    if (length(line) == 1) {
+      lines <- as.data.frame(unlist(strsplit(as.character(line[ncol]), ";")),
+                             stringsAsFactors = F)
     } else {
-      if (ncol==1) {                                #first column
-        lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
-      } else if (ncol==length(line)) {                 #last column
-        lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
+      if (ncol == 1) {    #first column
+        lines <- suppressWarnings(cbind(unlist(strsplit(
+          as.character(line[ncol]), ";")), line[2:length(line)]))
+      } else if (ncol == length(line)) {                 #last column
+        lines <- suppressWarnings(cbind(line[1:ncol - 1],
+                      unlist(strsplit(as.character(line[ncol]), ";"))))
       } else {
-        lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
+        lines <- suppressWarnings(cbind(line[1:ncol - 1],
+            unlist(strsplit(as.character(line[ncol]), ";"), use.names = F),
+            line[(ncol + 1):length(line)]))
       }
     }
-    colnames(lines)=header
+    colnames(lines) <- header
     return(lines)
   } else {
     return(line)
   }
 }
 
-#create new lines if there's more than one id per cell in the columns in order to have only one id per line
-one_id_one_line <-function(tab,ncol){
-  
-  if (ncol(tab)>1){
-    
-    tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
-    header=colnames(tab)
-    res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
-    for (i in 1:nrow(tab) ) {
-      lines = split_ids_per_line(tab[i,],ncol)
-      res = rbind(res,lines)
+#create new lines if there's more than one id per cell in the columns in order
+# to have only one id per line
+one_id_one_line <- function(tab, ncol) {
+
+  if (ncol(tab) > 1) {
+
+    tab[, ncol] <- sapply(tab[, ncol], function(x) gsub("[[:blank:]]", "", x))
+    header <- colnames(tab)
+    res <- as.data.frame(matrix(ncol = ncol(tab), nrow = 0))
+    for (i in seq_len(nrow(tab))) {
+      lines <- split_ids_per_line(tab[i, ], ncol)
+      res <- rbind(res, lines)
     }
-  }else {
-    res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
-    res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
-    colnames(res)=colnames(tab)
+  } else {
+    res <- unlist(sapply(tab[, 1], function(x) strsplit(x, ";")), use.names = F)
+    res <- data.frame(res[which(!is.na(res[res != ""]))], stringsAsFactors = F)
+    colnames(res) <- colnames(tab)
   }
   return(res)
 }
 
 get_limit <- function(mat) {
-  min = min(apply(mat,2,min,na.rm=TRUE))
-  max = max(apply(mat,2,max,na.rm=TRUE))
-  return(c(min,max))
+  min <- min(apply(mat, 2, min, na.rm = TRUE))
+  max <- max(apply(mat, 2, max, na.rm = TRUE))
+  return(c(min, max))
 }
 
-check_pathway_ids<- function(pathways_ids) {
-  problematic_pathways <- c("04215","04723")
-  to_remove <- intersect(pathways_ids,problematic_pathways)
-  if (length(to_remove) > 0){ print(paste("Pathway(s)",to_remove,"have been remove from input")) }
+check_pathway_ids <- function(pathways_ids) {
+  problematic_pathways <- c("04215", "04723")
+  to_remove <- intersect(pathways_ids, problematic_pathways)
+  if (length(to_remove) > 0) {
+    print(paste("Pathway(s)", to_remove, "have been remove from input"))
+    }
   pathways_ids <- pathways_ids[which(!pathways_ids %in% problematic_pathways)]
-  if (length(pathways_ids) == 0){stop("No pathways ids to process")}
-  return (pathways_ids)
+  if (length(pathways_ids) == 0) {
+    stop("No pathways ids to process")
+    }
+  return(pathways_ids)
 }
 
-get_args <- function(){
-  
+get_args <- function() {
+
   ## Collect arguments
   args <- commandArgs(TRUE)
-  
+
   ## Default setting when no arguments passed
-  if(length(args) < 1) {
+  if (length(args) < 1) {
     args <- c("--help")
   }
-  
+
   ## Help section
-  if("--help" %in% args) {
+  if ("--help" %in% args) {
     cat("Pathview R script
     Arguments:
       --help                  Print this test
-      --input                 path of the input  file (must contains a colum of uniprot and/or geneID accession number)
+      --input                 path of the input  file (must contains a colum of
+                              uniprot and/or geneid accession number)
       --id_list               list of ids to use, ',' separated
-      --pathways_id           Id(s) of pathway(s) to use, if several, semicolon separated list : hsa00010;hsa05412 
-      --id_type               Type of accession number ('uniprotID' or 'geneID')
-      --id_column             Column containing accesion number of interest (ex : 'c1')
+      --pathways_id           Id(s) of pathway(s) to use, if several, semicolon
+                              separated list : hsa00010;hsa05412
+      --id_type               Type of accession number ('uniprotid' or 'geneid')
+      --id_column             Column containing accesion number of interest
+                              (ex : 'c1')
       --header                Boolean, TRUE if header FALSE if not
       --output                Output filename
-      --fold_change_col       Column(s) containing fold change values (comma separated)
+      --fold_change_col       Column(s) containing fold change values
+                              (comma separated)
       --native_kegg           TRUE : native KEGG graph, FALSE : Graphviz graph
       --species               KEGG species (hsa, mmu, ...)
-      --pathways_input        Tab with pathways in a column, output format of find_pathways
+      --pathways_input        Tab with pathways in a column, output format of
+                              find_pathways
       --pathway_col           Column of pathways to use
       --header2               Boolean, TRUE if header FALSE if not
-      --pathways_list         path of file containg the species pathways list (hsa_pathways.loc, mmu_pathways.loc, ...)
+      --pathways_list         path of file containg the species pathways list
+                              (hsa_pathways.loc, mmu_pathways.loc, ...)
 
       Example:
-      ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n")
-    
-    q(save="no")
+      ./PathView.R --input 'input.csv' --pathway_id '05412'
+        --id_type 'uniprotid' --id_column 'c1' --header TRUE \n\n")
+
+    q(save = "no")
   }
-  
-  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
-  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
-  args <- as.list(as.character(argsDF$V2))
-  names(args) <- argsDF$V1
-  
+
+  parseargs <- function(x) strsplit(sub("^--", "", x), "=")
+  argsdf <- as.data.frame(do.call("rbind", parseargs(args)))
+  args <- as.list(as.character(argsdf$V2))
+  names(args) <- argsdf$V1
+
   return(args)
 }
 
-main <- function(){
-  
+main <- function() {
+
   args <- get_args()
-  
-  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda")
-  #load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda")
-  
+
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/
+  #kegg_maps_visualization/args.Rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/
+  #kegg_maps_visualization/args.Rda")
+
   ###setting variables
-  if (!is.null(args$pathways_id)) { 
+  if (!is.null(args$pathways_id)) {
     ids <- get_list_from_cp(clean_bad_character(args$pathways_id))
-    ids <- sapply(ids, function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
-  }else if (!is.null(args$pathways_input)){
+    ids <- sapply(ids, function(x) remove_kegg_prefix(x), USE.NAMES = FALSE)
+  }else if (!is.null(args$pathways_input)) {
     header2 <- str2bool(args$header2)
-    pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col))
-    pathways_file = read_file(args$pathways_input,header2)
-    ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
+    pathway_col <- as.numeric(gsub("c", "", args$pathway_col))
+    pathways_file <- read_file(args$pathways_input, header2)
+    ids <- sapply(rapply(strsplit(clean_bad_character(
+      pathways_file[, pathway_col]), ","), c),
+      function(x) remove_kegg_prefix(x), USE.NAMES = FALSE)
   }
-  if (args$native_kegg) {ids = check_pathway_ids(ids)} #remove problematic pathways
-  pathways_list <- read_file(args$pathways_list,F)
+  if (args$native_kegg) {
+    ids <- check_pathway_ids(ids)
+    } #remove problematic pathways
+  pathways_list <- read_file(args$pathways_list, F)
   if (!is.null(args$id_list)) {
     id_list <- get_list_from_cp(args$id_list)
     }
   id_type <- tolower(args$id_type)
-  ncol <- as.numeric(gsub("c", "" ,args$id_column))
+  ncol <- as.numeric(gsub("c", "", args$id_column))
   header <- str2bool(args$header)
   native_kegg <- str2bool(args$native_kegg)
-  species=args$species
-  fold_change_data = str2bool(args$fold_change_data)
-  
-  #org list used in mapped2geneID
-  org <- c('Hs','Mm','Rn')
-  names(org) <- c('hsa','mmu','rno')
-  
+  species <- args$species
+  fold_change_data <- str2bool(args$fold_change_data)
+
+  #org list used in mapped2geneid
+  org <- c("Hs", "Mm", "Rn")
+  names(org) <- c("hsa", "mmu", "rno")
+
   #read input file or list
-  if (!is.null(args$input)){
-    tab <- read_file(args$input,header)
-    tab <- data.frame(tab[which(tab[ncol]!=""),],stringsAsFactors = F)
-    tab = one_id_one_line(tab,ncol)
+  if (!is.null(args$input)) {
+    tab <- read_file(args$input, header)
+    tab <- data.frame(tab[which(tab[ncol] != ""), ], stringsAsFactors = F)
+    tab <- one_id_one_line(tab, ncol)
   } else {
-    id_list = gsub("[[:blank:]]|\u00A0|NA","",id_list)
-    id_list = unique(id_list[id_list!=""])
-    tab <- data.frame(id_list,stringsAsFactors = F)
-    ncol=1
+    id_list <- gsub("[[:blank:]]|\u00A0|NA", "", id_list)
+    id_list <- unique(id_list[id_list != ""])
+    tab <- data.frame(id_list, stringsAsFactors = F)
+    ncol <- 1
   }
-  
-  
-  ##### map uniprotID to entrez geneID and kegg to geneID
-  uniprotID=""
-  mapped2geneID=""
+
+
+  ##### map uniprotid to entrez geneid and kegg to geneid
+  uniprotid <- ""
+  mapped2geneid <- ""
   if (id_type == "uniprotid") {
-    uniprotID=tab[,ncol]
-    mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL)
-    geneID = mapped2geneID[,2]
-    tab = cbind(tab,geneID)
-    ncol=ncol(tab)
-  }else if (id_type == "keggid"){
-    keggID = tab[,ncol]  
-    geneID = kegg_to_geneID(keggID)
-    tab = cbind(tab,geneID)
-    ncol=ncol(tab)
-  }else if (id_type == "geneid"){
-    colnames(tab)[ncol] <- "geneID"
+    uniprotid <- tab[, ncol]
+    mapped2geneid <- id2eg(ids = uniprotid, category = "uniprot",
+                           org = org[[species]], pkg.name = NULL)
+    geneid <- mapped2geneid[, 2]
+    tab <- cbind(tab, geneid)
+    ncol <- ncol(tab)
+  }else if (id_type == "keggid") {
+    keggid <- tab[, ncol]
+    geneid <- kegg_to_geneid(keggid)
+    tab <- cbind(tab, geneid)
+    ncol <- ncol(tab)
+  }else if (id_type == "geneid") {
+    colnames(tab)[ncol] <- "geneid"
   }
-  
+
   ##### build matrix to map on KEGG pathway (kgml : KEGG xml)
-  geneID_indices = which(!is.na(tab$geneID))
+  geneid_indices <- which(!is.na(tab$geneid))
   if (fold_change_data) {
-    fold_change <- as.integer(unlist(strsplit(gsub("c","",args$fold_change_col),",")))
-    if (length(fold_change) > 3) { fold_change= fold_change[1:3] }
-    if (length(fold_change)==1){
-      tab[,fold_change] <- as.double(gsub(",",".",as.character(tab[,fold_change]) ))
+    fold_change <- as.integer(unlist(strsplit(gsub("c", "",
+                                            args$fold_change_col), ",")))
+    if (length(fold_change) > 3) {
+      fold_change <- fold_change[1:3]
+      }
+    if (length(fold_change) == 1) {
+      tab[, fold_change] <- as.double(gsub(
+                     ",", ".", as.character(tab[, fold_change])))
     } else {
-      tab[,fold_change] <- apply(tab[,fold_change],2,function(x) as.double(gsub(",",".",as.character(x))))
+      tab[, fold_change] <- apply(tab[, fold_change], 2,
+                        function(x) as.double(gsub(",", ".", as.character(x))))
     }
-    mat = tab[geneID_indices,c(ncol,fold_change)]
-    mat = mat[(!duplicated(mat$geneID)),]
-    geneID=mat$geneID
-    mat = as.data.frame(mat[,-1])
-    row.names(mat)=geneID
-    limit = get_limit(mat)
+    mat <- tab[geneid_indices, c(ncol, fold_change)]
+    mat <- mat[(!duplicated(mat$geneid)), ]
+    geneid <- mat$geneid
+    mat <- as.data.frame(mat[, -1])
+    row.names(mat) <- geneid
+    limit <- get_limit(mat)
   } else {
-    mat = unique(as.character(tab$geneID[!is.na(tab$geneID[tab$geneID!=""])]))
-    geneID=mat
-    limit=1
+    mat <- unique(as.character(
+           tab$geneid[!is.na(tab$geneid[tab$geneid != ""])]))
+    geneid <- mat
+    limit <- 1
   }
-  
-  #####mapping geneID (with or without expression values) on KEGG pathway
-  plot.col.key= TRUE
-  low_color = "green"
-  mid_color = "#F3F781" #yellow
-  high_color = "red"
+
+  #####mapping geneid (with or without expression values) on KEGG pathway
+  plot_col_key <- TRUE
+  low_color <- "green"
+  mid_color <- "#F3F781" #yellow
+  high_color <- "red"
   if (!fold_change_data) {
-    plot.col.key= FALSE   #if there's no exrepession data, we don't show the color key
-    high_color = "#81BEF7" #blue
-  } 
-  
+    plot_col_key <- FALSE
+    #if there's no exrepession data, we don't show the color key
+    high_color <- "#81BEF7" #blue
+  }
+
   #create graph(s) and text output
   for (id in ids) {
-    suffix= get_suffix(pathways_list,species,id)
-    pv.out <- suppressMessages(pathview(gene.data = mat,
-             gene.idtype = "entrez", 
+    suffix <- get_suffix(pathways_list, species, id)
+    pv_out <- suppressMessages(pathview(gene.data = mat,
+             gene.idtype = "entrez",
              pathway.id = id,
-             species = species, 
-             kegg.dir = ".", 
-             out.suffix=suffix,
+             species = species,
+             kegg.dir = ".",
+             out.suffix = suffix,
              kegg.native = native_kegg,
-             low = list(gene = low_color, cpd = "blue"), 
-             mid = list(gene = mid_color, cpd = "transparent"), 
-             high = list(gene = high_color, cpd = "yellow"), 
-             na.col="#D8D8D8", #gray
-             cpd.data=NULL,
-             plot.col.key = plot.col.key,
-             pdf.size=c(9,9),
-             limit=list(gene=limit, cpd=limit)))
-    
-    if (is.list(pv.out)){
-    
+             low = list(gene = low_color, cpd = "blue"),
+             mid = list(gene = mid_color, cpd = "transparent"),
+             high = list(gene = high_color, cpd = "yellow"),
+             na.col = "#D8D8D8", #gray
+             cpd.data = NULL,
+             plot_col_key = plot_col_key,
+             pdf.size = c(9, 9),
+             limit = list(gene = limit, cpd = limit)))
+
+    if (is.list(pv_out)) {
+
       #creating text file
-      if (!exists("DF")) { 
-        DF <- data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F)
+      if (!exists("df")) {
+        df <- data.frame(t(mapping_summary(pv_out, species, id, id_type,
+                  pathways_list, geneid, uniprotid, mapped2geneid)),
+                  stringsAsFactors = F, check.names = F)
       } else {
-        #print (mapping_summary(pv.out,species,id))
-        DF <- rbind(DF,data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F))
+        df <- rbind(df, data.frame(t(mapping_summary(pv_out, species, id,
+                    id_type, pathways_list, geneid, uniprotid, mapped2geneid)),
+                    stringsAsFactors = F, check.names = F))
       }
     }
   }
-  
-  DF <- as.data.frame(apply(DF, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
-  
+
+  df <- as.data.frame(apply(df, c(1, 2),
+                  function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
+
   #text file output
-  write.table(DF,file=args$output,quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
+  write.table(df, file = args$output, quote = FALSE, sep = "\t",
+              row.names = FALSE, col.names = TRUE)
 }
 
 main()