Mercurial > repos > proteore > proteore_maps_visualization

annotate kegg_maps_visualization.R @ 12:10c572ad2b9e draft default tip

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"planemo upload commit 209e9e48505e55a2a2b4b1d7b053f557344bc2e8-dirty"
author proteore
date Mon, 10 May 2021 12:45:44 +0000
parents 7d04efde2526
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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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10 read_file <- function(path, header) {
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11 file <- try(read.csv(path, header = header, sep = "\t",
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12 stringsAsFactors = FALSE, quote = "\"", check.names = F,
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13 comment.char = ""), silent = TRUE)
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14 if (inherits(file, "try-error")) {
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15 stop("Read file error! Please check your file (header, # character, etc)")
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16 }else {
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17 return(file)
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18 }
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19 }
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21 ##### fuction to clean and concatenate pathway name
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22 ##### (allow more flexibility for user input)
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23 concat_string <- function(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 <- gsub("\\'", "", x)
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30 x <- gsub("\\(.*)", "", x)
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31 x <- gsub("\\/", "", x)
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32 x <- tolower(x)
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33 return(x)
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34 }
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35
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36 #return output suffix (pathway name) from id kegg (ex : hsa:00010)
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37 get_suffix <- function(pathways_list, species, id) {
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38 suffix <- gsub("/", "or", pathways_list[pathways_list[, 1] == paste(
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39 species, id, sep = ""), 2])
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40 suffix <- gsub(" ", "_", suffix)
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41 if (nchar(suffix) > 50) {
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42 suffix <- substr(suffix, 1, 50)
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43 }
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44 return(suffix)
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45 }
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46
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47 str2bool <- function(x) {
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48 if (any(is.element(c("t", "true"), tolower(x)))) {
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49 return(TRUE)
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50 }else if (any(is.element(c("f", "false"), tolower(x)))) {
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51 return(FALSE)
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52 }else {
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53 return(NULL)
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54 }
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55 }
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56
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57 is_letter <- function(x) grepl("[[:alpha:]]", x)
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59 remove_kegg_prefix <- function(x) {
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60 x <- gsub(":", "", x)
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61 if (substr(x, 1, 4) == "path") {
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62 x <- substr(x, 5, nchar(x))
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63 }
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64 if (is_letter(substr(x, 1, 3))) {
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65 x <- substr(x, 4, nchar(x))
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66 }
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67 return(x)
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68 }
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69
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70 kegg_to_geneid <- function(vector) {
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71 #nolint start
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72 vector <- sapply(vector, function(x) unlist(
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73 strsplit(x, ":"))[2], USE.NAMES = F)
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74 #nolint end
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75 return(vector)
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76 }
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77
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78 clean_bad_character <- function(string) {
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79 string <- gsub("X", "", string)
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80 return(string)
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81 }
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82
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83 get_list_from_cp <- function(list) {
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84 list <- gsub(";", "\t", list)
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85 list <- gsub(",", "\t", list)
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86 list <- strsplit(list, "[ \t\n]+")[[1]]
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87 list <- list[list != ""] #remove empty entry
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88 list <- gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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89 return(list)
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90 }
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91
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92 get_ref_pathways <- function(species) {
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93 ##all available pathways for the species
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94 pathways <- keggLink("pathway", species)
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95 tot_path <- unique(pathways)
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96
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97 ##formating the dat into a list object
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98 ##key= pathway ID, value = genes of the pathway in the kegg format
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99 pathways_list <- sapply(tot_path, function(pathway)
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100 names(which(pathways == pathway)))
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101 return(pathways_list)
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102 }
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103
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104 #nolint start
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105 mapping_summary <- function(pv_out, species, id, id_type, pathways_list,
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106 geneid, uniprotid, mapped2geneid) {
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107 ref_pathways <- get_ref_pathways(species)
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108 names(ref_pathways) <- sapply(names(ref_pathways), function(x)
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109 gsub("path:[a-z]{3}", "", x), USE.NAMES = F)
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110 #nolint end
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111 #genes present in pathway
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112 genes <- ref_pathways[id][[1]]
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113 nb_genes <- length(genes)
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114
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115 #genes mapped on pathway genes
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116 mapped <- unlist(sapply(pv_out$plot.data.gene$all.mapped,
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117 function(x) strsplit(x, ",")), use.names = F)
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118 mapped <- unique(mapped[mapped != ""])
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119 nb_mapped <- length(mapped)
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120
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121 #compute ratio of mapping
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122 ratio <- round((nb_mapped / nb_genes) * 100, 2)
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123 if (is.nan(ratio)) {
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124 ratio <- ""
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125 }
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126 pathway_id <- paste(species, id, sep = "")
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127 pathway_name <- as.character(
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128 pathways_list[pathways_list[, 1] == pathway_id, ][2])
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129
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130 if (id_type == "geneid" || id_type == "keggid") {
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131 row <- c(pathway_id, pathway_name, length(unique(geneid)),
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132 nb_mapped, nb_genes, ratio, paste(mapped, collapse = ";"))
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133 names(row) <- c("KEGG pathway ID", "pathway name",
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134 "nb of Entrez gene ID used", "nb of Entrez gene ID mapped",
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135 "nb of Entrez gene ID in the pathway",
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136 "ratio of Entrez gene ID mapped (%)",
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137 "Entrez gene ID mapped")
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138 } else if (id_type == "uniprotid") {
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139 row <- c(pathway_id, pathway_name, length(unique(uniprotid)),
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140 length(unique(geneid)), nb_mapped, nb_genes, ratio,
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141 paste(mapped, collapse = ";"),
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142 paste(mapped2geneid[which(mapped2geneid[, 2] %in% mapped)],
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143 collapse = ";"))
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144 names(row) <- c("KEGG pathway ID", "pathway name", "nb of Uniprot_AC used",
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145 "nb of Entrez gene ID used", "nb of Entrez gene ID mapped",
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146 "nb of Entrez gene ID in the pathway",
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147 "ratio of Entrez gene ID mapped (%)",
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148 "Entrez gene ID mapped", "uniprot_AC mapped")
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149 }
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150 return(row)
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151 }
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152
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153 #take data frame, return data frame
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154 split_ids_per_line <- function(line, ncol) {
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155
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156 #print (line)
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157 header <- colnames(line)
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158 line[ncol] <- gsub("[[:blank:]]|\u00A0", "", line[ncol])
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159
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160 if (length(unlist(strsplit(as.character(line[ncol]), ";"))) > 1) {
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161 if (length(line) == 1) {
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162 lines <- as.data.frame(unlist(strsplit(as.character(line[ncol]), ";")),
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163 stringsAsFactors = F)
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164 } else {
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165 if (ncol == 1) { #first column
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166 lines <- suppressWarnings(cbind(unlist(strsplit(
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167 as.character(line[ncol]), ";")), line[2:length(line)]))
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168 } else if (ncol == length(line)) { #last column
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169 lines <- suppressWarnings(cbind(line[1:ncol - 1],
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170 unlist(strsplit(as.character(line[ncol]), ";"))))
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171 } else {
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172 lines <- suppressWarnings(cbind(line[1:ncol - 1],
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173 unlist(strsplit(as.character(line[ncol]), ";"), use.names = F),
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174 line[(ncol + 1):length(line)]))
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175 }
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176 }
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177 colnames(lines) <- header
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178 return(lines)
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179 } else {
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180 return(line)
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181 }
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182 }
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183
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184 #create new lines if there's more than one id per cell in the columns in order
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185 # to have only one id per line
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186 one_id_one_line <- function(tab, ncol) {
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187
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188 if (ncol(tab) > 1) {
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189
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190 tab[, ncol] <- sapply(tab[, ncol], function(x) gsub("[[:blank:]]", "", x))
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191 header <- colnames(tab)
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192 res <- as.data.frame(matrix(ncol = ncol(tab), nrow = 0))
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193 for (i in seq_len(nrow(tab))) {
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194 lines <- split_ids_per_line(tab[i, ], ncol)
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195 res <- rbind(res, lines)
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196 }
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197 } else {
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198 res <- unlist(sapply(tab[, 1], function(x) strsplit(x, ";")), use.names = F)
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199 res <- data.frame(res[which(!is.na(res[res != ""]))], stringsAsFactors = F)
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200 colnames(res) <- colnames(tab)
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201 }
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202 return(res)
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203 }
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204
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205 get_limit <- function(mat) {
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206 min <- min(apply(mat, 2, min, na.rm = TRUE))
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207 max <- max(apply(mat, 2, max, na.rm = TRUE))
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208 return(c(min, max))
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209 }
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210
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211 check_pathway_ids <- function(pathways_ids) {
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212 problematic_pathways <- c("04215", "04723")
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213 to_remove <- intersect(pathways_ids, problematic_pathways)
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214 if (length(to_remove) > 0) {
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215 print(paste("Pathway(s)", to_remove, "have been remove from input"))
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216 }
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217 pathways_ids <- pathways_ids[which(!pathways_ids %in% problematic_pathways)]
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218 if (length(pathways_ids) == 0) {
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219 stop("No pathways ids to process")
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220 }
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221 return(pathways_ids)
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222 }
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223
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224 get_args <- function() {
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225
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226 ## Collect arguments
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227 args <- commandArgs(TRUE)
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228
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229 ## Default setting when no arguments passed
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230 if (length(args) < 1) {
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231 args <- c("--help")
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232 }
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233
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234 ## Help section
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235 if ("--help" %in% args) {
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236 cat("Pathview R script
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237 Arguments:
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238 --help Print this test
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239 --input path of the input file (must contains a colum of
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240 uniprot and/or geneid accession number)
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241 --id_list list of ids to use, ',' separated
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242 --pathways_id Id(s) of pathway(s) to use, if several, semicolon
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243 separated list : hsa00010;hsa05412
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244 --id_type Type of accession number ('uniprotid' or 'geneid')
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245 --id_column Column containing accesion number of interest
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246 (ex : 'c1')
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247 --header Boolean, TRUE if header FALSE if not
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248 --output Output filename
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249 --fold_change_col Column(s) containing fold change values
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250 (comma separated)
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251 --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph
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252 --species KEGG species (hsa, mmu, ...)
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253 --pathways_input Tab with pathways in a column, output format of
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254 find_pathways
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255 --pathway_col Column of pathways to use
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256 --header2 Boolean, TRUE if header FALSE if not
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257 --pathways_list path of file containg the species pathways list
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258 (hsa_pathways.loc, mmu_pathways.loc, ...)
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259
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260 Example:
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261 ./PathView.R --input 'input.csv' --pathway_id '05412'
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262 --id_type 'uniprotid' --id_column 'c1' --header TRUE \n\n")
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263
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264 q(save = "no")
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265 }
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266
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267 parseargs <- function(x) strsplit(sub("^--", "", x), "=")
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268 argsdf <- as.data.frame(do.call("rbind", parseargs(args)))
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269 args <- as.list(as.character(argsdf$V2))
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270 names(args) <- argsdf$V1
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271
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272 return(args)
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273 }
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274
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275 main <- function() {
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276
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277 args <- get_args()
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278
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279 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/
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280 #kegg_maps_visualization/args.Rda")
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281 #load("/home/dchristiany/proteore_project/ProteoRE/tools/
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282 #kegg_maps_visualization/args.Rda")
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283
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284 ###setting variables
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285 if (!is.null(args$pathways_id)) {
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286 ids <- get_list_from_cp(clean_bad_character(args$pathways_id))
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287 ids <- sapply(ids, function(x) remove_kegg_prefix(x), USE.NAMES = FALSE)
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288 }else if (!is.null(args$pathways_input)) {
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289 header2 <- str2bool(args$header2)
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290 pathway_col <- as.numeric(gsub("c", "", args$pathway_col))
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291 pathways_file <- read_file(args$pathways_input, header2)
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292 ids <- sapply(rapply(strsplit(clean_bad_character(
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293 pathways_file[, pathway_col]), ","), c),
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294 function(x) remove_kegg_prefix(x), USE.NAMES = FALSE)
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295 }
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296 if (args$native_kegg) {
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297 ids <- check_pathway_ids(ids)
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298 } #remove problematic pathways
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299 pathways_list <- read_file(args$pathways_list, F)
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300 if (!is.null(args$id_list)) {
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301 id_list <- get_list_from_cp(args$id_list)
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302 }
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303 id_type <- tolower(args$id_type)
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304 ncol <- as.numeric(gsub("c", "", args$id_column))
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305 header <- str2bool(args$header)
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306 native_kegg <- str2bool(args$native_kegg)
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307 species <- args$species
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308 fold_change_data <- str2bool(args$fold_change_data)
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309
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310 #org list used in mapped2geneid
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311 org <- c("Hs", "Mm", "Rn")
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312 names(org) <- c("hsa", "mmu", "rno")
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313
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314 #read input file or list
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315 if (!is.null(args$input)) {
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316 tab <- read_file(args$input, header)
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317 tab <- data.frame(tab[which(tab[ncol] != ""), ], stringsAsFactors = F)
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318 tab <- one_id_one_line(tab, ncol)
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319 } else {
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320 id_list <- gsub("[[:blank:]]|\u00A0|NA", "", id_list)
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321 id_list <- unique(id_list[id_list != ""])
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322 tab <- data.frame(id_list, stringsAsFactors = F)
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323 ncol <- 1
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324 }
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325
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326
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327 ##### map uniprotid to entrez geneid and kegg to geneid
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328 uniprotid <- ""
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329 mapped2geneid <- ""
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330 if (id_type == "uniprotid") {
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331 uniprotid <- tab[, ncol]
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332 mapped2geneid <- id2eg(ids = uniprotid, category = "uniprot",
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333 org = org[[species]], pkg.name = NULL)
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334 geneid <- mapped2geneid[, 2]
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335 tab <- cbind(tab, geneid)
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336 ncol <- ncol(tab)
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337 }else if (id_type == "keggid") {
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338 keggid <- tab[, ncol]
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339 geneid <- kegg_to_geneid(keggid)
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340 tab <- cbind(tab, geneid)
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341 ncol <- ncol(tab)
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342 }else if (id_type == "geneid") {
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343 colnames(tab)[ncol] <- "geneid"
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344 }
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345
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346 ##### build matrix to map on KEGG pathway (kgml : KEGG xml)
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347 geneid_indices <- which(!is.na(tab$geneid))
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348 if (fold_change_data) {
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349 fold_change <- as.integer(unlist(strsplit(gsub("c", "",
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350 args$fold_change_col), ",")))
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351 if (length(fold_change) > 3) {
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352 fold_change <- fold_change[1:3]
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353 }
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354 if (length(fold_change) == 1) {
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355 tab[, fold_change] <- as.double(gsub(
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356 ",", ".", as.character(tab[, fold_change])))
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357 } else {
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358 tab[, fold_change] <- apply(tab[, fold_change], 2,
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359 function(x) as.double(gsub(",", ".", as.character(x))))
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360 }
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361 mat <- tab[geneid_indices, c(ncol, fold_change)]
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362 mat <- mat[(!duplicated(mat$geneid)), ]
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363 geneid <- mat$geneid
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364 mat <- as.data.frame(mat[, -1])
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365 row.names(mat) <- geneid
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366 limit <- get_limit(mat)
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367 } else {
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368 mat <- unique(as.character(
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369 tab$geneid[!is.na(tab$geneid[tab$geneid != ""])]))
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370 geneid <- mat
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371 limit <- 1
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372 }
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373
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374 #####mapping geneid (with or without expression values) on KEGG pathway
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375 plot_col_key <- TRUE
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376 low_color <- "green"
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377 mid_color <- "#F3F781" #yellow
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378 high_color <- "red"
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379 if (!fold_change_data) {
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380 plot_col_key <- FALSE
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381 #if there's no exrepession data, we don't show the color key
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382 high_color <- "#81BEF7" #blue
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383 }
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384
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385 #create graph(s) and text output
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386 for (id in ids) {
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387 suffix <- get_suffix(pathways_list, species, id)
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388 pv_out <- suppressMessages(pathview(gene.data = mat,
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389 gene.idtype = "entrez",
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390 pathway.id = id,
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391 species = species,
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392 kegg.dir = ".",
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393 out.suffix = suffix,
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394 kegg.native = native_kegg,
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395 low = list(gene = low_color, cpd = "blue"),
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396 mid = list(gene = mid_color, cpd = "transparent"),
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397 high = list(gene = high_color, cpd = "yellow"),
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398 na.col = "#D8D8D8", #gray
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399 cpd.data = NULL,
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400 plot_col_key = plot_col_key,
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401 pdf.size = c(9, 9),
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402 limit = list(gene = limit, cpd = limit)))
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403
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404 if (is.list(pv_out)) {
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405
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406 #creating text file
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407 if (!exists("df")) {
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408 df <- data.frame(t(mapping_summary(pv_out, species, id, id_type,
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409 pathways_list, geneid, uniprotid, mapped2geneid)),
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410 stringsAsFactors = F, check.names = F)
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411 } else {
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412 df <- rbind(df, data.frame(t(mapping_summary(pv_out, species, id,
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413 id_type, pathways_list, geneid, uniprotid, mapped2geneid)),
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414 stringsAsFactors = F, check.names = F))
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415 }
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416 }
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417 }
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418
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419 df <- as.data.frame(apply(df, c(1, 2),
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420 function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA
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421
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422 #text file output
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423 write.table(df, file = args$output, quote = FALSE, sep = "\t",
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424 row.names = FALSE, col.names = TRUE)
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425 }
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426
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427 main()