Mercurial > repos > proteore > proteore_maps_visualization

annotate kegg_maps_visualization.R @ 3:dfceadc0b703 draft

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author proteore
date Fri, 28 Jun 2019 05:16:30 -0400
parents 6f389729a30b
children 8e611bdc96ec
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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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6 options(warn=-1) #TURN OFF WARNINGS !!!!!!
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7 suppressMessages(library("pathview"))
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8 suppressMessages(library(KEGGREST))
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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, comment.char = ""),silent=TRUE)
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12 if (inherits(file,"try-error")){
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13 stop("Read file error ! Please check your file (header, # character, etc) ")
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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 kegg_to_geneID <- function(vector){
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68 vector <- sapply(vector, function(x) unlist(strsplit(x,":"))[2],USE.NAMES = F)
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69 return (vector)
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70 }
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71
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72 clean_bad_character <- function(string) {
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73 string <- gsub("X","",string)
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74 return(string)
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75 }
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76
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77 get_list_from_cp <-function(list){
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78 list = gsub(";","\t",list)
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79 list = gsub(",","\t",list)
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80 list = strsplit(list, "[ \t\n]+")[[1]]
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81 list = list[list != ""] #remove empty entry
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82 list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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83 return(list)
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84 }
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85
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86 get_ref_pathways <- function(species){
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87 ##all available pathways for the species
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88 pathways <-keggLink("pathway", species)
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89 tot_path<-unique(pathways)
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90
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91 ##formating the dat into a list object
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92 ##key= pathway ID, value = genes of the pathway in the kegg format
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93 pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway)))
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94 return (pathways_list)
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95 }
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96
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97 mapping_summary <- function(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID){
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98 ref_pathways = get_ref_pathways(species)
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99 names(ref_pathways) <- sapply(names(ref_pathways), function(x) gsub("path:[a-z]{3}","",x),USE.NAMES = F)
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100
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101 #genes present in pathway
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102 genes = ref_pathways[id][[1]]
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103 nb_genes = length(genes)
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104
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105 #genes mapped on pathway genes
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106 mapped <- unlist(sapply(pv.out$plot.data.gene$all.mapped, function(x) strsplit(x,",")),use.names = F)
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107 mapped = unique(mapped[mapped!=""])
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108 nb_mapped <- length(mapped)
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109
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110 #compue ratio of mapping
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111 ratio = round((nb_mapped/nb_genes)*100, 2)
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112 if (is.nan(ratio)) { ratio = ""}
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113 pathway_id = paste(species,id,sep="")
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114 pathway_name = as.character(pathways_list[pathways_list[,1]==pathway_id,][2])
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115
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116 if (id_type=="geneid" || id_type=="keggid") {
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117 row <- c(pathway_id,pathway_name,length(unique(geneID)),nb_mapped,nb_genes,ratio,paste(mapped,collapse=";"))
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118 names(row) <- c("KEGG pathway ID","pathway name","nb of Entrez gene ID used","nb of Entrez gene ID mapped",
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119 "nb of Entrez gene ID in the pathway", "ratio of Entrez gene ID mapped (%)","Entrez gene ID mapped")
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120 } else if (id_type=="uniprotid") {
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121 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=";"))
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122 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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123 "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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124 }
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125 return(row)
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126 }
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127
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128 #take data frame, return data frame
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129 split_ids_per_line <- function(line,ncol){
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130
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131 #print (line)
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132 header = colnames(line)
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133 line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol])
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134
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135 if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
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136 if (length(line)==1 ) {
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137 lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
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138 } else {
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139 if (ncol==1) { #first column
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140 lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
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141 } else if (ncol==length(line)) { #last column
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142 lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
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143 } else {
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144 lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
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145 }
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146 }
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147 colnames(lines)=header
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148 return(lines)
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149 } else {
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150 return(line)
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151 }
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152 }
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153
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154 #create new lines if there's more than one id per cell in the columns in order to have only one id per line
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155 one_id_one_line <-function(tab,ncol){
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156
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157 if (ncol(tab)>1){
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158
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159 tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
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160 header=colnames(tab)
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161 res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
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162 for (i in 1:nrow(tab) ) {
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163 lines = split_ids_per_line(tab[i,],ncol)
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164 res = rbind(res,lines)
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165 }
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166 }else {
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167 res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
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168 res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
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169 colnames(res)=colnames(tab)
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170 }
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171 return(res)
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172 }
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173
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174 get_limit <- function(mat) {
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175 min = min(apply(mat,2,min))
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176 max = max(apply(mat,2,max))
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177 return(c(min,max))
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178 }
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179
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180 get_args <- function(){
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181
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182 ## Collect arguments
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183 args <- commandArgs(TRUE)
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184
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185 ## Default setting when no arguments passed
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186 if(length(args) < 1) {
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187 args <- c("--help")
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188 }
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189
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190 ## Help section
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191 if("--help" %in% args) {
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192 cat("Pathview R script
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193 Arguments:
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194 --help Print this test
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195 --input path of the input file (must contains a colum of uniprot and/or geneID accession number)
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196 --id_list list of ids to use, ',' separated
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197 --pathways_id Id(s) of pathway(s) to use, if several, semicolon separated list : hsa00010;hsa05412
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198 --id_type Type of accession number ('uniprotID' or 'geneID')
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199 --id_column Column containing accesion number of interest (ex : 'c1')
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200 --header Boolean, TRUE if header FALSE if not
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201 --output Output filename
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202 --fold_change_col Column(s) containing fold change values (comma separated)
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203 --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph
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204 --species KEGG species (hsa, mmu, ...)
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205 --pathways_input Tab with pathways in a column, output format of find_pathways
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206 --pathway_col Column of pathways to use
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207 --header2 Boolean, TRUE if header FALSE if not
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208 --pathways_list path of file containg the species pathways list (hsa_pathways.loc, mmu_pathways.loc, ...)
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209
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210 Example:
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211 ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n")
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212
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213 q(save="no")
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214 }
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215
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216 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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217 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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218 args <- as.list(as.character(argsDF$V2))
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219 names(args) <- argsDF$V1
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220
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221 return(args)
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222 }
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223
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224 main <- function(){
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225
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226 args <- get_args()
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227
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228 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda")
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229 #load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_maps_visualization/args.Rda")
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230
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231 ###setting variables
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232 if (!is.null(args$pathways_id)) {
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233 ids <- get_list_from_cp(clean_bad_character(args$pathways_id))
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parents:
diff changeset
234 ids <- sapply(ids, function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
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proteore
parents:
diff changeset
235 }else if (!is.null(args$pathways_input)){
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proteore
parents:
diff changeset
236 header2 <- str2bool(args$header2)
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proteore
parents:
diff changeset
237 pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col))
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proteore
parents:
diff changeset
238 pathways_file = read_file(args$pathways_input,header2)
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proteore
parents:
diff changeset
239 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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parents:
diff changeset
240 }
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proteore
parents:
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241 pathways_list <- read_file(args$pathways_list,F)
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parents:
diff changeset
242 if (!is.null(args$id_list)) {
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proteore
parents:
diff changeset
243 id_list <- get_list_from_cp(args$id_list)
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proteore
parents:
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244 }
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proteore
parents:
diff changeset
245 id_type <- tolower(args$id_type)
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proteore
parents:
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246 ncol <- as.numeric(gsub("c", "" ,args$id_column))
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proteore
parents:
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247 header <- str2bool(args$header)
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parents:
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248 native_kegg <- str2bool(args$native_kegg)
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parents:
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249 species=args$species
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250 fold_change_data = str2bool(args$fold_change_data)
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251
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parents:
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252 #org list used in mapped2geneID
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parents:
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253 org <- c('Hs','Mm','Rn')
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parents:
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254 names(org) <- c('hsa','mmu','rno')
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255
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parents:
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256 #read input file or list
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proteore
parents:
diff changeset
257 if (!is.null(args$input)){
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parents:
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258 tab <- read_file(args$input,header)
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proteore
parents:
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259 tab <- data.frame(tab[which(tab[ncol]!=""),],stringsAsFactors = F)
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parents:
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260 tab = one_id_one_line(tab,ncol)
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parents:
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261 } else {
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parents:
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262 id_list = gsub("[[:blank:]]|\u00A0|NA","",id_list)
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proteore
parents:
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263 id_list = unique(id_list[id_list!=""])
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proteore
parents:
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264 tab <- data.frame(id_list,stringsAsFactors = F)
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parents:
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265 ncol=1
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parents:
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266 }
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proteore
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diff changeset
267
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268
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parents:
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269 ##### map uniprotID to entrez geneID and kegg to geneID
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parents:
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270 uniprotID=""
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271 mapped2geneID=""
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parents:
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272 if (id_type == "uniprotid") {
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proteore
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273 uniprotID=tab[,ncol]
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parents:
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274 mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL)
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parents:
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275 geneID = mapped2geneID[,2]
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parents:
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276 tab = cbind(tab,geneID)
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parents:
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277 ncol=ncol(tab)
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proteore
parents:
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278 }else if (id_type == "keggid"){
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parents:
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279 keggID = tab[,ncol]
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280 geneID = kegg_to_geneID(keggID)
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proteore
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281 tab = cbind(tab,geneID)
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282 ncol=ncol(tab)
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proteore
parents:
diff changeset
283 }else if (id_type == "geneid"){
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proteore
parents:
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284 colnames(tab)[ncol] <- "geneID"
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parents:
diff changeset
285 }
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286
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proteore
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287 ##### build matrix to map on KEGG pathway (kgml : KEGG xml)
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288 geneID_indices = which(!is.na(tab$geneID))
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parents:
diff changeset
289 if (fold_change_data) {
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proteore
parents:
diff changeset
290 fold_change <- as.integer(unlist(strsplit(gsub("c","",args$fold_change_col),",")))
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proteore
parents:
diff changeset
291 if (length(fold_change) > 3) { fold_change= fold_change[1:3] }
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proteore
parents:
diff changeset
292 if (length(fold_change)==1){
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proteore
parents:
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293 tab[,fold_change] <- as.double(gsub(",",".",as.character(tab[,fold_change]) ))
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294 } else {
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295 tab[,fold_change] <- apply(tab[,fold_change],2,function(x) as.double(gsub(",",".",as.character(x))))
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296 }
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297 mat = tab[geneID_indices,c(ncol,fold_change)]
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298 mat = mat[(!duplicated(mat$geneID)),]
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diff changeset
299 geneID=mat$geneID
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parents:
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300 mat = as.data.frame(mat[,-1])
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diff changeset
301 row.names(mat)=geneID
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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parents:
diff changeset
302 limit = get_limit(mat)
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proteore
parents:
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303 } else {
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
304 mat = unique(as.character(tab$geneID[!is.na(tab$geneID[tab$geneID!=""])]))
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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305 geneID=mat
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
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306 limit=1
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diff changeset
307 }
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308
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309 #####mapping geneID (with or without expression values) on KEGG pathway
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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parents:
diff changeset
310 plot.col.key= TRUE
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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parents:
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311 low_color = "green"
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parents:
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312 mid_color = "#F3F781" #yellow
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parents:
diff changeset
313 high_color = "red"
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proteore
parents:
diff changeset
314 if (!fold_change_data) {
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proteore
parents:
diff changeset
315 plot.col.key= FALSE #if there's no exrepession data, we don't show the color key
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316 high_color = "#81BEF7" #blue
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proteore
parents:
diff changeset
317 }
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318
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319 #create graph(s) and text output
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
320 for (id in ids) {
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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321 suffix= get_suffix(pathways_list,species,id)
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parents:
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322 pv.out <- suppressMessages(pathview(gene.data = mat,
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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323 gene.idtype = "entrez",
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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parents:
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324 pathway.id = id,
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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325 species = species,
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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parents:
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326 kegg.dir = ".",
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327 out.suffix=suffix,
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328 kegg.native = native_kegg,
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parents:
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329 low = list(gene = low_color, cpd = "blue"),
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parents:
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330 mid = list(gene = mid_color, cpd = "transparent"),
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331 high = list(gene = high_color, cpd = "yellow"),
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332 na.col="#D8D8D8", #gray
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diff changeset
333 cpd.data=NULL,
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proteore
parents:
diff changeset
334 plot.col.key = plot.col.key,
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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335 pdf.size=c(9,9),
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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parents:
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336 limit=list(gene=limit, cpd=limit)))
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337
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338 if (is.list(pv.out)){
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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parents:
diff changeset
339
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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340 #creating text file
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
341 if (!exists("DF")) {
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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342 DF <- data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F)
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parents:
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343 } else {
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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344 #print (mapping_summary(pv.out,species,id))
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diff changeset
345 DF <- rbind(DF,data.frame(t(mapping_summary(pv.out,species,id,id_type,pathways_list,geneID,uniprotID,mapped2geneID)),stringsAsFactors = F,check.names = F))
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346 }
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proteore
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347 }
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proteore
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348 }
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349
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
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350 DF <- as.data.frame(apply(DF, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
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351
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
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352 #text file output
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
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353 write.table(DF,file=args$output,quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
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354 }
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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355
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
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356 main()