annotate kegg_maps_visualization.R @ 6:eb140217a9f1 draft default tip

"planemo upload commit 1f9a98db2496834cc38a281cbe3d4b11de2bc3d2-dirty"

#!/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"))
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{
      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)
}

kegg_to_geneID <- function(vector){
  vector <- sapply(vector, function(x) unlist(strsplit(x,":"))[2],USE.NAMES = F)
  return (vector)
}

clean_bad_character <- function(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")
  return(list)
}

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)
}

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)
  
  #genes present in pathway
  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!=""])
  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")
  } 
  return(row)
}

#take data frame, return  data frame
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)
    } 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]),";"))))
      } else {
        lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
      }
    }
    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)
    }
  }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))
}

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)
}

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)
}

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")
  
  ###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)
  }
  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))
  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]!=""),],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
  }
  
  
  ##### 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"
  }
  
  ##### build matrix to map on KEGG pathway (kgml : KEGG xml)
  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]) ))
    } else {
      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)
  } else {
    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"
  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
  } 
  
  #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),
             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)
      } 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 <- 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)
}

main()