Mercurial > repos > proteore > proteore_pathview_mapping

annotate kegg_pathways_visualization.R @ 12:9fe4a861601b draft

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planemo upload commit 7e2bd28d27e13c402acd46500f64d5c117797aa7-dirty
author proteore
date Fri, 09 Nov 2018 05:11:46 -0500
parents
children da82872f5c80
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12
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1 #!/usr/bin/Rscript
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2 #Rscript made for mapping genesID on KEGG pathway with Pathview package
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3 #input : csv file containing ids (uniprot or geneID) to map, plus parameters
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4 #output : KEGG pathway : jpeg or pdf file.
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5
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6 options(warn=-1) #TURN OFF WARNINGS !!!!!!
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7
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8 suppressMessages(library("pathview"))
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9
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10 read_file <- function(path,header){
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11 file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
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12 if (inherits(file,"try-error")){
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13 stop("File not found !")
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14 }else{
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15 return(file)
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16 }
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17 }
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18
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19 ##### fuction to clean and concatenate pathway name (allow more flexibility for user input)
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20 concat_string <- function(x){
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21 x <- gsub(" - .*","",x)
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22 x <- gsub(" ","",x)
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23 x <- gsub("-","",x)
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24 x <- gsub("_","",x)
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25 x <- gsub(",","",x)
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26 x <- gsub("\\'","",x)
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27 x <- gsub("\\(.*)","",x)
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28 x <- gsub("\\/","",x)
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29 x <- tolower(x)
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30 return(x)
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31 }
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32
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33 #return output suffix (pathway name) from id kegg (ex : hsa:00010)
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34 get_suffix <- function(pathways_list,species,id){
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35 suffix = gsub("/","or",pathways_list[pathways_list[,1]==paste(species,id,sep=""),2])
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36 suffix = gsub(" ","_",suffix)
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37 if (nchar(suffix) > 50){
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38 suffix = substr(suffix,1,50)
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39 }
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40 return(suffix)
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41 }
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42
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43 str2bool <- function(x){
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44 if (any(is.element(c("t","true"),tolower(x)))){
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45 return (TRUE)
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46 }else if (any(is.element(c("f","false"),tolower(x)))){
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47 return (FALSE)
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48 }else{
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49 return(NULL)
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50 }
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51 }
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52
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53 is.letter <- function(x) grepl("[[:alpha:]]", x)
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54
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55 #### hsa00010 -> 00010
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56 remove_kegg_prefix <- function(x){
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57 x = gsub(":","",x)
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58 if (substr(x,1,4) == 'path'){
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59 x=substr(x,5,nchar(x))
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60 }
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61 if (is.letter(substr(x,1,3))){
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62 x <- substr(x,4,nchar(x))
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63 }
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64 return(x)
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65 }
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66
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67 clean_bad_character <- function(string) {
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68 string <- gsub("X","",string)
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69 return(string)
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70 }
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71
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72 get_list_from_cp <-function(list){
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73 list = strsplit(list, "[ \t\n]+")[[1]]
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74 list = list[list != ""] #remove empty entry
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75 list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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76 return(list)
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77 }
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78
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79 #return a summary from the mapping with pathview in a vector
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80 mapping_summary <- function(pv.out,species,id,id_type){
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81
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82 mapped <- pv.out$plot.data.gene$kegg.names[which(pv.out$plot.data.gene$all.mapped!='')]
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83 nb_mapped <- length(mapped)
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84 nb_kegg_id <- length(unique(pv.out$plot.data.gene$kegg.names))
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85 ratio = round((nb_mapped/nb_kegg_id)*100, 2)
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86 if (is.nan(ratio)) { ratio = ""}
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87 pathway_id = paste(species,id,sep="")
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88 pathway_name = as.character(pathways_list[pathways_list[,1]==pathway_id,][2])
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89
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90 if (id_type=="geneid"){
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91 row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_kegg_id,nb_mapped,ratio,paste(mapped,collapse=";"))
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92 names(row) <- c("KEGG pathway ID","pathway name","nb of Entrez gene ID used","nb of Entrez gene ID mapped",
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93 "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped")
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94 }else if (id_type=="uniprotid"){
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95 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=";"))
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96 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",
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97 "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped","uniprot_AC mapped")
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98 }
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99 return(row)
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100 }
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101
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102 get_args <- function(){
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103
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104 ## Collect arguments
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105 args <- commandArgs(TRUE)
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106
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107 ## Default setting when no arguments passed
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108 if(length(args) < 1) {
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109 args <- c("--help")
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110 }
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111
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112 ## Help section
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113 if("--help" %in% args) {
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114 cat("Pathview R script
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115 Arguments:
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116 --help Print this test
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117 --input path of the input file (must contains a colum of uniprot and/or geneID accession number)
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118 --id_list list of ids to use, ',' separated
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119 --pathways_id Id(s) of pathway(s) to use, if several, semicolon separated list : hsa00010;hsa05412
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120 --id_type Type of accession number ('uniprotID' or 'geneID')
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121 --id_column Column containing accesion number of interest (ex : 'c1')
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122 --header Boolean, TRUE if header FALSE if not
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123 --output Output filename
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124 --fold_change_col Column(s) containing fold change values (comma separated)
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125 --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph
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126 --species KEGG species (hsa, mmu, ...)
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127 --pathways_input Tab with pathways in a column, output format of find_pathways
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128 --pathway_col Column of pathways to use
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129 --header2 Boolean, TRUE if header FALSE if not
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130 --pathways_list path of file containg the species pathways list (hsa_pathways.loc, mmu_pathways.loc, ...)
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131
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132 Example:
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133 ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n")
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134
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135 q(save="no")
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136 }
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137
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138 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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139 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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140 args <- as.list(as.character(argsDF$V2))
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141 names(args) <- argsDF$V1
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142
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143 return(args)
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144 }
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145
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146 args <- get_args()
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147
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148 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_visualization/args.Rda")
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149 #load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_visualization/args.Rda")
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150
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151 ###setting variables
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152 if (!is.null(args$pathways_id)) {
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153 ids <- get_list_from_cp(clean_bad_character(args$pathways_id))
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154 ids <- sapply(ids, function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
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155 }else if (!is.null(args$pathways_input)){
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156 header2 <- str2bool(args$header2)
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157 pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col))
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158 pathways_file = read_file(args$pathways_input,header2)
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159 ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
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160 }
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161 pathways_list <- read_file(args$pathways_list,F)
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162 if (!is.null(args$id_list)) {
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163 id_list <- get_list_from_cp(args$id_list)
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164 }
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165 id_type <- tolower(args$id_type)
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166 ncol <- as.numeric(gsub("c", "" ,args$id_column))
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167 header <- str2bool(args$header)
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168 native_kegg <- str2bool(args$native_kegg)
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169 species=args$species
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170 fold_change_data = str2bool(args$fold_change_data)
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171
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172 #org list used in mapped2geneID
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173 org <- c('Hs','Mm','Rn')
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174 names(org) <- c('hsa','mmu','rno')
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175
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176 #read input file or list
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177 if (!is.null(args$input)){
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178 tab <- read_file(args$input,header)
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179 tab <- data.frame(tab[which(tab[ncol]!=""),])
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180 } else {
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181 tab <- data.frame(id_list,stringsAsFactors = F)
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182 ncol=1
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183 }
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184
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185 #fold change columns
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186 #make sure its double and name expression value columns
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187 if (fold_change_data){
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188 fold_change <- as.integer(unlist(strsplit(gsub("c","",args$fold_change_col),",")))
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189 if (length(fold_change) > 3) { fold_change= fold_change[1:3] }
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190 for (i in 1:length(fold_change)) {
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191 fc_col = fold_change[i]
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192 colnames(tab)[fc_col] <- paste("e",i,sep='')
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193 tab[,fc_col] <- as.double(gsub(",",".",as.character(tab[,fc_col]) ))
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194 }
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195 }
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196
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197 ##### map uniprotID to entrez geneID
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198 if (id_type == "uniprotid") {
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199 uniprotID = tab[,ncol]
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200 mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL)
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201 geneID = mapped2geneID[,2]
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202 tab = cbind(tab,geneID)
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203 }else if (id_type == "geneid"){
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204 colnames(tab)[ncol] <- "geneID"
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205 }
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206
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207 geneID = as.character(tab$geneID[which(!is.na(tab$geneID))])
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208 geneID = gsub(" ","",geneID)
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209 geneID = unlist(strsplit(geneID,"[;]"))
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210
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211 ##### build matrix to map on KEGG pathway (kgml : KEGG xml)
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212 if (fold_change_data) {
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213 geneID_indices = which(!duplicated(geneID))
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214 if (length(fold_change) == 3){
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215 mat <- as.data.frame(cbind(tab$e1,tab$e2,tab$e3)[which(!is.na(tab$geneID)),])
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216 mat = mat[geneID_indices,]
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217 row.names(mat) <- geneID[geneID_indices]
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218 } else if (length(fold_change) == 2){
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219 mat <- as.data.frame(cbind(tab$e1,tab$e2)[which(!is.na(tab$geneID)),])
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220 mat = mat[geneID_indices,]
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221 row.names(mat) <- geneID[geneID_indices]
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222 } else {
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223 mat <- as.data.frame(cbind(tab$e1)[which(!is.na(tab$geneID)),])
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224 mat = mat[geneID_indices,]
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225 names(mat) <- geneID[geneID_indices]
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226 }
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227 } else {
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228 mat <- geneID
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229 }
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230
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231 #####mapping geneID (with or without expression values) on KEGG pathway
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232 plot.col.key= TRUE
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233 low_color = "green"
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234 mid_color = "#F3F781" #yellow
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235 high_color = "red"
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236 if (is.null(tab$e1)) {
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237 plot.col.key= FALSE #if there's no exrepession data, we don't show the color key
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238 high_color = "#81BEF7" #blue
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239 }
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240
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241 #create graph(s) and text output
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242 for (id in ids) {
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243 suffix= get_suffix(pathways_list,species,id)
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244 pv.out <- suppressMessages(pathview(gene.data = mat,
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245 gene.idtype = "entrez",
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246 pathway.id = id,
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247 species = species,
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248 kegg.dir = ".",
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249 out.suffix=suffix,
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250 kegg.native = native_kegg,
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251 low = list(gene = low_color, cpd = "blue"),
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252 mid = list(gene = mid_color, cpd = "transparent"),
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253 high = list(gene = high_color, cpd = "yellow"),
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254 na.col="#D8D8D8", #gray
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255 cpd.data=NULL,
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256 plot.col.key = plot.col.key,
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257 pdf.size=c(9,9)))
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258
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259 if (is.list(pv.out)){
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260
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261 #creating text file
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262 if (!exists("DF")) {
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263 DF <- data.frame(t(mapping_summary(pv.out,species,id,id_type)),stringsAsFactors = F,check.names = F)
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264 } else {
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265 #print (mapping_summary(pv.out,species,id))
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266 DF <- rbind(DF,data.frame(t(mapping_summary(pv.out,species,id,id_type)),stringsAsFactors = F,check.names = F))
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267 }
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268 }
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269
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270 }
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271
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272 DF <- as.data.frame(apply(DF, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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273
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274 #text file output
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275 write.table(DF,file=args$output,quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)