Mercurial > repos > proteore > proteore_pathview_mapping

annotate PathView.R @ 11:6d5c0ff2b0bd draft

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planemo upload commit 3cfb63ac3585431e7cdcc0a0bd11c33b946a6751-dirty
author proteore
date Fri, 14 Sep 2018 09:52:28 -0400
parents e8d6e50f5d38
children
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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 suppressMessages(library("pathview"))
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7
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8 read_file <- function(path,header){
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9 file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote=""),silent=TRUE)
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10 if (inherits(file,"try-error")){
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11 stop("File not found !")
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12 }else{
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13 return(file)
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14 }
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15 }
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16
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17 ##### fuction to clean and concatenate pathway name (allow more flexibility for user input)
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18 concat_string <- function(x){
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19 x <- gsub(" - .*","",x)
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20 x <- gsub(" ","",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 <- tolower(x)
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28 return(x)
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29 }
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30
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31
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32 get_args <- function(){
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33
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34 ## Collect arguments
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35 args <- commandArgs(TRUE)
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36
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37 ## Default setting when no arguments passed
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38 if(length(args) < 1) {
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39 args <- c("--help")
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40 }
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41
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42 ## Help section
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43 if("--help" %in% args) {
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44 cat("Pathview R script
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45 Arguments:
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46 --help Print this test
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47 --input path of the input file (must contains a colum of uniprot and/or geneID accession number)
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48 --id_list list of ids to use, ',' separated
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49 --pathways_id Id(s) of pathway(s) to use, if several, semicolon separated list : hsa00010;hsa05412
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50 --id_type Type of accession number ('uniprotID' or 'geneID')
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51 --id_column Column containing accesion number of interest (ex : 'c1')
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52 --header Boolean, TRUE if header FALSE if not
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53 --ouput Output filename
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54 --expression_values1 Column containing expression values (first condition)
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55 --expression_values2 Column containing expression values (second condition)
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56 --expression_values3 Column containing expression values (third condition)
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57 --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph
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58 --species KEGG species (hsa, mmu, ...)
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59 --pathways_input Tab with pathways in a column, output format of find_pathways
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60 --pathway_col Column of pathways to use
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61 --header2 Boolean, TRUE if header FALSE if not
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62
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63 Example:
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64 ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n")
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65
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66 q(save="no")
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67 }
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68
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69 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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70 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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71 args <- as.list(as.character(argsDF$V2))
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72 names(args) <- argsDF$V1
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73
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74 return(args)
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75 }
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76
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77 str2bool <- function(x){
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78 if (any(is.element(c("t","true"),tolower(x)))){
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79 return (TRUE)
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80 }else if (any(is.element(c("f","false"),tolower(x)))){
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81 return (FALSE)
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82 }else{
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83 return(NULL)
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84 }
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85 }
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86
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87 is.letter <- function(x) grepl("[[:alpha:]]", x)
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88
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89 #### hsa00010 -> 00010
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90 remove_kegg_prefix <- function(x){
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91 x = gsub(":","",x)
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92 if (substr(x,1,4) == 'path'){
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93 x=substr(x,5,nchar(x))
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94 }
0
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95 if (is.letter(substr(x,1,3))){
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96 x <- substr(x,4,nchar(x))
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97 }
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98 return(x)
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99 }
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100
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101 clean_bad_character <- function(string) {
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102 string <- gsub("X","",string)
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103 string <- gsub(" ","",string)
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104 return(string)
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105 }
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106
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107 args <- get_args()
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108
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109 ###setting variables
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110 if (!is.null(args$pathways_id)) {
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111 ids <- sapply(rapply(strsplit(clean_bad_character(args$pathways_id),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
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112 }else if (!is.null(args$pathways_input)){
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113 header2 <- str2bool(args$header2)
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114 pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col))
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115 pathways_file = read_file(args$pathways_input,header2)
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116 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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117 }
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118 #if (!is.null(args$pathways_name)) {names <- as.vector(sapply(strsplit(args$pathways_name,","), function(x) concat_string(x),USE.NAMES = FALSE))}
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119 if (!is.null(args$id_list)) {id_list <- as.vector(strsplit(clean_bad_character(args$id_list),","))}
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120 id_type <- tolower(args$id_type)
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121 ncol <- as.numeric(gsub("c", "" ,args$id_column))
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122 header <- str2bool(args$header)
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123 #output <- args$output
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124 native_kegg <- str2bool(args$native_kegg)
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125 species=args$species
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126 #org list used in mapped2geneID
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127 org <- c('Hs','Mm')
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128 names(org) <- c('hsa','mmu')
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129
0
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130
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131
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132 #read input file or list
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133 if (!is.null(args$input)){
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134 tab <- read_file(args$input,header)
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135 tab <- data.frame(tab[which(tab[ncol]!=""),])
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136 } else {
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137 tab <- data.frame(id_list)
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138 ncol=1
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139 }
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140
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141 e1 <- as.numeric(gsub("c", "" ,args$expression_values1))
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142 if (!is.null(args$expression_values1)) { colnames(tab)[e1] <- "e1" }
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143 e2 <- as.numeric(gsub("c", "" ,args$expression_values2))
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144 if (!is.null(args$expression_values2)) { colnames(tab)[e2] <- "e2" }
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145 e3 <- as.numeric(gsub("c", "" ,args$expression_values3))
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146 if (!is.null(args$expression_values3)) { colnames(tab)[e3] <- "e3" }
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147
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148
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149 ##### map uniprotID to entrez geneID
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150 if (id_type == "uniprotid") {
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151
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152 uniprotID = tab[,ncol]
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153 mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL)
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154 geneID = mapped2geneID[,2]
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155 tab = cbind(tab,geneID)
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156
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157 }else if (id_type == "geneid"){
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158
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159 colnames(tab)[ncol] <- "geneID"
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160
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161 }
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162
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163 geneID = tab$geneID[which(tab$geneID !="NA")]
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164 geneID = gsub(" ","",geneID)
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165 geneID = unlist(strsplit(geneID,"[;]"))
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166
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167
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168 #### get hsa pathways list
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169 #download.file(url = "http://rest.kegg.jp/link/pathway/hsa", destfile = "/home/dchristiany/proteore_project/ProteoRE/tools/pathview/geneID_to_hsa_pathways.csv")
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170 #geneid_hsa_pathways <- read_file(path = "/home/dchristiany/proteore_project/ProteoRE/tools/pathview/geneID_to_hsa_pathways.csv",FALSE)
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171 #names(geneid_hsa_pathways) <- c("geneID","pathway")
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172
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173 ##### build matrix to map on KEGG pathway (kgml : KEGG xml)
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174 if (!is.null(args$expression_values1)&is.null(args$expression_values2)&is.null(args$expression_values3)){
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175 mat <- as.data.frame(cbind(tab$e1)[which(!is.na(tab$geneID)),])
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176 row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))]
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177 } else if (!is.null(args$expression_values1)&!is.null(args$expression_values2)&is.null(args$expression_values3)){
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178 mat <- as.data.frame(cbind(tab$e1,tab$e2)[which(!is.na(tab$geneID)),])
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179 row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))]
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180 }else if (!is.null(args$expression_values1)&!is.null(args$expression_values2)&!is.null(args$expression_values3)){
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181 mat <- as.data.frame(cbind(tab$e1,tab$e2,tab$e3)[which(!is.na(tab$geneID)),])
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182 row.names(mat) <- tab$geneID[which(!is.na(tab$geneID))]
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183 } else {
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184 mat <- geneID
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185 }
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186
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187
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188 #### simulation data test
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189 #exp1 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=100)
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190 #exp2 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=50)
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191 #exp3 <- sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL, species="hsa", discrete = FALSE, nmol = 161, nexp = 1, rand.seed=10)
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192 #tab <- cbind(tab,exp1,exp2,exp3)
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193
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194 #write.table(tab, file='/home/dchristiany/proteore_project/ProteoRE/tools/pathview/Lacombe_sim_expression_data.tsv', quote=FALSE, sep='\t',row.names = FALSE)
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195
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196 #mat <- exp1[1:nrow(tab)]
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197 #names(mat) <- geneID
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198
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199
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200 #####mapping geneID (with or without expression values) on KEGG pathway
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201 plot.col.key= TRUE
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202 low_color = "green"
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203 mid_color = "#F3F781" #yellow
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204 high_color = "red"
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205 if (is.null(tab$e1)) {
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206 plot.col.key= FALSE #if there's no exrepession data, we don't show the color key
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207 high_color = "#81BEF7" #blue
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208 }
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209
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210 for (id in ids) {
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211 pathview(gene.data = mat,
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212 pathway.id = id,
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213 species = species,
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214 kegg.dir = ".",
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215 gene.idtype = "entrez",
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216 kegg.native = native_kegg,
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217 low = list(gene = low_color, cpd = "blue"),
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218 mid = list(gene = mid_color, cpd = "transparent"),
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219 high = list(gene = high_color, cpd = "yellow"),
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220 na.col="#D8D8D8", #gray
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221 cpd.data=NULL,
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222 plot.col.key = plot.col.key,
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223 pdf.size=c(9,9))
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224 }
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225
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226 ########using keggview.native
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227
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228 #xml.file=system.file("extdata", "hsa00010.xml", package = "pathview")
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229 #node.data=node.info("/home/dchristiany/hsa00010.xml")
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230 #plot.data.gene=node.map(mol.data=test, node.data, node.types="gene")
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231 #colors =node.color(plot.data = plot.data.gene[,1:9])