--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kegg_pathways_visualization.R	Fri Nov 09 05:11:46 2018 -0500
@@ -0,0 +1,275 @@
+#!/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
+#output : KEGG pathway : jpeg or pdf file.
+
+options(warn=-1)  #TURN OFF WARNINGS !!!!!!
+
+suppressMessages(library("pathview"))
+
+read_file <- function(path,header){
+    file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
+    if (inherits(file,"try-error")){
+      stop("File not found !")
+    }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)
+  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)
+  }
+  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{
+    return(NULL)
+  }
+}
+
+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))
+  }
+  if (is.letter(substr(x,1,3))){
+    x <- substr(x,4,nchar(x))
+  }
+  return(x)
+}
+
+clean_bad_character <- function(string)  {
+  string <- gsub("X","",string)
+  return(string)
+}
+
+get_list_from_cp <-function(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)
+}
+
+#return a summary from the mapping with pathview in a vector
+mapping_summary <- function(pv.out,species,id,id_type){
+  
+  mapped <- pv.out$plot.data.gene$kegg.names[which(pv.out$plot.data.gene$all.mapped!='')]
+  nb_mapped <- length(mapped)
+  nb_kegg_id <- length(unique(pv.out$plot.data.gene$kegg.names))
+  ratio = round((nb_mapped/nb_kegg_id)*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"){
+    row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_kegg_id,nb_mapped,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_kegg_id,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)
+}
+
+get_args <- function(){
+  
+  ## Collect arguments
+  args <- commandArgs(TRUE)
+  
+  ## Default setting when no arguments passed
+  if(length(args) < 1) {
+    args <- c("--help")
+  }
+  
+  ## Help section
+  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)
+      --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')
+      --header                Boolean, TRUE if header FALSE if not
+      --output                Output filename
+      --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
+      --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, ...)
+
+      Example:
+      ./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
+  
+  return(args)
+}
+
+args <- get_args()
+
+#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_visualization/args.Rda")
+#load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_visualization/args.Rda")
+
+###setting variables
+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$pathways_input)){
+  header2 <- str2bool(args$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)
+}
+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$id_column))
+header <- str2bool(args$header)
+native_kegg <- str2bool(args$native_kegg)
+species=args$species
+fold_change_data = str2bool(args$fold_change_data)
+
+#org list used in mapped2geneID
+org <- c('Hs','Mm','Rn')
+names(org) <- c('hsa','mmu','rno')
+
+#read input file or list
+if (!is.null(args$input)){
+  tab <- read_file(args$input,header)
+  tab <- data.frame(tab[which(tab[ncol]!=""),])
+} else {
+  tab <- data.frame(id_list,stringsAsFactors = F)
+  ncol=1
+}
+
+#fold change columns
+#make sure its double and name expression value columns
+if (fold_change_data){
+  fold_change <- as.integer(unlist(strsplit(gsub("c","",args$fold_change_col),",")))
+  if (length(fold_change) > 3) { fold_change= fold_change[1:3] } 
+  for (i in 1:length(fold_change)) {
+    fc_col = fold_change[i]
+    colnames(tab)[fc_col] <- paste("e",i,sep='')
+    tab[,fc_col] <- as.double(gsub(",",".",as.character(tab[,fc_col]) ))
+  }
+}
+
+##### map uniprotID to entrez geneID
+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)
+}else if (id_type == "geneid"){
+  colnames(tab)[ncol] <- "geneID"
+}
+
+geneID = as.character(tab$geneID[which(!is.na(tab$geneID))])
+geneID = gsub(" ","",geneID)
+geneID = unlist(strsplit(geneID,"[;]"))
+
+##### build matrix to map on KEGG pathway (kgml : KEGG xml)
+if (fold_change_data) {
+  geneID_indices = which(!duplicated(geneID))
+  if (length(fold_change) == 3){
+    mat <- as.data.frame(cbind(tab$e1,tab$e2,tab$e3)[which(!is.na(tab$geneID)),])
+    mat = mat[geneID_indices,]
+    row.names(mat) <- geneID[geneID_indices]
+  } else if (length(fold_change) == 2){
+    mat <- as.data.frame(cbind(tab$e1,tab$e2)[which(!is.na(tab$geneID)),])
+    mat = mat[geneID_indices,]
+    row.names(mat) <- geneID[geneID_indices]
+  } else {
+    mat <- as.data.frame(cbind(tab$e1)[which(!is.na(tab$geneID)),])
+    mat = mat[geneID_indices,]
+    names(mat) <- geneID[geneID_indices]
+  }
+} else {
+  mat <- geneID
+}
+
+#####mapping geneID (with or without expression values) on KEGG pathway
+plot.col.key= TRUE
+low_color = "green"
+mid_color = "#F3F781" #yellow
+high_color = "red"
+if (is.null(tab$e1)) {
+  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", 
+           pathway.id = id,
+           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)))
+  
+  if (is.list(pv.out)){
+  
+    #creating text file
+    if (!exists("DF")) {
+      DF <- data.frame(t(mapping_summary(pv.out,species,id,id_type)),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)),stringsAsFactors = F,check.names = F))
+    }
+  }
+    
+}
+
+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)