Mercurial > repos > proteore > proteore_topgo

annotate topGO_enrichment.R @ 16:7f1ce70f0f09 draft default tip

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"planemo upload commit 29a04769c0546be759c38bbcc157c8bc09ec1115-dirty"
author proteore
date Mon, 17 May 2021 14:40:03 +0000
parents 8eaa43ba1bfc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 options(warn = -1) #TURN OFF WARNINGS !!!!!!
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2
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3 suppressMessages(library(ggplot2))
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4 suppressMessages(library(topGO))
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5
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6 get_args <- function() {
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7
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8 ## Collect arguments
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9 args <- commandArgs(TRUE)
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11 ## Default setting when no arguments passed
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12 if (length(args) < 1) {
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13 args <- c("--help")
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14 }
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15
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16 ## Help section
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17 if ("--help" %in% args) {
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18 cat("Pathview R script
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19 Arguments:
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20 --help Print this test
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21 --input_type
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22 --onto
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23 --option
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24 --correction
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25 --threshold
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26 --text
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27 --plot
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28 --column
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29 --geneuniverse
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30 --header
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31
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32 Example:
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33 Rscript --vanilla enrichment_v3.R --inputtype=tabfile (or copypaste)
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34 --input=file.txt --ontology='BP/CC/MF' --option=option
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35 (e.g : classic/elim...) --threshold=threshold --correction=correction
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36 --textoutput=text --barplotoutput=barplot --dotplotoutput=dotplot
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37 --column=column --geneuniver=human \n\n")
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38
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39 q(save = "no")
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40 }
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41
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42 parseargs <- function(x) strsplit(sub("^--", "", x), "=")
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43 argsdf <- as.data.frame(do.call("rbind", parseargs(args)))
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44 args <- as.list(as.character(argsdf$V2))
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45 names(args) <- argsdf$V1
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46
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47 return(args)
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48 }
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49
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50 read_file <- function(path, header) {
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51 file <- try(read.csv(path, header = header, sep = "\t",
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52 stringsAsFactors = FALSE, quote = "\"", check.names = F),
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53 silent = TRUE)
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54 if (inherits(file, "try-error")) {
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55 stop("File not found !")
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56 }else {
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57 return(file)
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58 }
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59 }
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60
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61 get_list_from_cp <- function(list) {
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62 list <- gsub(";", " ", list)
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63 list <- strsplit(list, "[ \t\n]+")[[1]]
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64 list <- list[list != ""] #remove empty entry
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65 list <- gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2")
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66 return(list)
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67 }
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68
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69 check_ens_ids <- function(vector) {
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70 ens_pattern <-
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71 "^(ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?
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72 |CG[0-9]+|[A-Z0-9]+\\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9])$"
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73 return(grepl(ens_pattern, vector))
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74 }
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75
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76 str2bool <- function(x) {
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77 if (any(is.element(c("t", "true"), tolower(x)))) {
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78 return(TRUE)
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79 }else if (any(is.element(c("f", "false"), tolower(x)))) {
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80 return(FALSE)
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81 }else {
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82 return(NULL)
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83 }
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84 }
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85
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86 # Some libraries such as GOsummaries won't be able to treat the values such as
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87 # "< 1e-30" produced by topGO. As such it is important to delete the < char
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88 # with the deleteinfchar function. Nevertheless the user will have access to
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89 #the original results in the text output.
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90 deleteinfchar <- function(values) {
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91
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92 lines <- grep("<", values)
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93 if (length(lines) != 0) {
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94 for (line in lines) {
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95 values[line] <- gsub("<", "", values[line])
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96 }
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97 }
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98 return(values)
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99 }
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100
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101 #nolint start
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102 corrMultipleTesting = function(result, mygodata, correction, threshold){
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103
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104 # adjust for multiple testing
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105 if (correction != "none"){
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106 # GenTable : transforms the result object into a list. Filters can be applied
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107 # (e.g : with the topNodes argument, to get for instance only the n first
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108 # GO terms with the lowest pvalues), but as we want to apply a correction we
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109 # take all the GO terms, no matter their pvalues
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110 allRes <- GenTable(mygodata, test = result, orderBy = "result",
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111 ranksOf = "result", topNodes = length(attributes(result)$score))
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112 # Some pvalues given by topGO are not numeric (e.g : "<1e-30). As such, these
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113 # values are converted to 1e-30 to be able to correct the pvalues
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114 pvaluestmp = deleteinfchar(allRes$test)
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115
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116 # the correction is done from the modified pvalues
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117 allRes$qvalues = p.adjust(pvaluestmp, method = as.character(correction),
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118 n = length(pvaluestmp))
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119 allRes = as.data.frame(allRes)
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120
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121 # Rename the test column by pvalues, so that is more explicit
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122 nb = which(names(allRes) %in% c("test"))
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123
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124 names(allRes)[nb] = "pvalues"
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125
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126 allRes = allRes[which(as.numeric(allRes$pvalues) <= threshold), ]
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127 if (length(allRes$pvalues) == 0) {
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128 print("Threshold was too stringent, no GO term found with pvalue
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129 equal or lesser than the threshold value")
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130 return(NULL)
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131 }
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132 allRes = allRes[order(allRes$qvalues), ]
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133 }
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134
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135 if (correction == "none"){
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136 # get all the go terms under user threshold
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137 mysummary <- summary(attributes(result)$score <= threshold)
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138 numsignif <- as.integer(mysummary[[3]])
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139 # get all significant nodes
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140 allRes <- GenTable(mygodata, test = result, orderBy = "result",
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141 ranksOf = "result", topNodes = numsignif)
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142
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143
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144 allRes = as.data.frame(allRes)
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145 # Rename the test column by pvalues, so that is more explicit
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146 nb = which(names(allRes) %in% c("test"))
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147 names(allRes)[nb] = "pvalues"
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148 if (numsignif == 0) {
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149
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150 print("Threshold was too stringent, no GO term found with pvalue
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151 equal or lesser than the threshold value")
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152 return(NULL)
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153 }
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154
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155 allRes = allRes[order(allRes$pvalues), ]
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156 }
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157
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158 return(allRes)
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159 }
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160 #nolint end
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161
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162 #roundvalues will simplify the results by rounding down the values.
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163 #For instance 1.1e-17 becomes 1e-17
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164 roundvalues <- function(values) {
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165 for (line in seq_len(length(values))) {
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166 values[line] <- as.numeric(gsub(".*e", "1e", as.character(values[line])))
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167 }
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168 return(values)
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169 }
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170
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171 #nolint start
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172 createDotPlot = function(data, onto) {
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173
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174 values = deleteinfchar(data$pvalues)
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175 values = roundvalues(values)
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176 values = as.numeric(values)
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177
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178 geneRatio = data$Significant / data$Annotated
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179 goTerms = data$Term
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180 count = data$Significant
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181
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182 labely = paste("GO terms", onto, sep = " ")
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183 ggplot(data, aes(x = geneRatio, y = goTerms, color = values, size=count)) + geom_point( ) + scale_colour_gradientn( colours = c("red", "violet", "blue")) + xlab("Gene Ratio") + ylab(labely) + labs(color = "p-values\n" )
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184 ggsave("dotplot.png", device = "png", dpi = 320, limitsize = TRUE,
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185 width = 15, height = 15, units = "cm")
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186 }
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187
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188 createBarPlot = function(data, onto) {
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189
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190 values = deleteinfchar(data$pvalues)
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191 values = roundvalues(values)
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192 values = as.numeric(values)
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193
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194 goTerms = data$Term
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195 count = data$Significant
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196
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197 labely = paste("GO terms", onto, sep=" ")
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198 ggplot(data, aes(x = goTerms, y = count, fill = values, scale(scale = 0.5))) + ylab("Gene count") + xlab(labely) + geom_bar(stat = "identity") + scale_fill_gradientn(colours = c("red","violet","blue")) + coord_flip() + labs(fill = "p-values\n")
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199 ggsave("barplot.png", device = "png", dpi = 320, limitsize = TRUE,
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200 width = 15, height = 15, units = "cm")
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201 }
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202
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203 #nolint end
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204
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205 # Produce the different outputs
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206 createoutputs <- function(result, cut_result, text, barplot, dotplot, onto) {
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207
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208 if (is.null(result)) {
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209 err_msg <- "None of the input ids can be found in the org package data,
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210 enrichment analysis cannot be realized. \n The inputs ids probably
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211 either have no associated GO terms or are not ENSG identifiers
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212 (e.g : ENSG00000012048)."
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213 write.table(err_msg, file = "result", quote = FALSE, sep = "\t",
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214 col.names = F, row.names = F)
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215 }else if (is.null(cut_result)) {
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216 err_msg <- "Threshold was too stringent, no GO term found with pvalue equal
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217 or lesser than the threshold value."
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218 write.table(err_msg, file = "result.tsv", quote = FALSE, sep = "\t",
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219 col.names = F, row.names = F)
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220 }else {
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221 write.table(cut_result, file = "result.tsv", quote = FALSE, sep = "\t",
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222 col.names = T, row.names = F)
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223
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224 if (barplot) {
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225 createBarPlot(cut_result, onto) #nolint
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226 }
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227 if (dotplot) {
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228 createDotPlot(cut_result, onto) #nolint
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229 }
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230 }
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231 }
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232
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233 # Launch enrichment analysis and return result data from the analysis or the
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234 # null object if the enrichment could not be done.
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235 goenrichment <- function(geneuniverse, sample, background_sample, onto) {
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236
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237 if (is.null(background_sample)) {
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238 xx <- annFUN.org(onto, mapping = geneuniverse, ID = "ensembl") #nolint
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239 #get all the GO terms of the corresponding ontology (BP/CC/MF)
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240 #and all their associated ensembl ids according to the org package
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241
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242 #nolint start
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243
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244 allGenes <- unique(unlist(xx))
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245 #check if the genes given by the user can be found in the org package
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246 #(gene universe), that is in allGenes
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247 } else {
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248 allGenes <- background_sample
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249 }
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250
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251 if (length(intersect(sample,allGenes)) == 0) {
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252 print("None of the input ids can be found in the org package data,
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253 enrichment analysis cannot be realized. \n The inputs ids probably
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254 have no associated GO terms.")
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255 return(c(NULL, NULL))
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256 }
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257
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258 geneList <- factor(as.integer(allGenes %in% sample))
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259 #duplicated ids in sample count only for one
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260 if (length(levels(geneList)) == 1 ){
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261 stop("All or none of the background genes are found in tested genes dataset,
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262 enrichment analysis can't be done")
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263 }
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264 names(geneList) <- allGenes
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265
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266 #nolint end
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267
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268 #topGO enrichment
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269
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270 # Creation of a topGOdata object
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271 # It will contain : the list of genes of interest, the GO annotations and
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272 # the GO hierarchy
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273 # Parameters :
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274 # ontology : character string specifying the ontology of interest (BP, CC, MF)
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275 # allGenes : named vector of type numeric or factor
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276 # annot : tells topGO how to map genes to GO annotations.
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277 # argument not used here : nodeSize : at which minimal number of GO
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278 # annotations do we consider a gene
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279
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280 mygodata <- new("topGOdata", description = "SEA with TopGO", ontology = onto,
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281 allGenes = geneList, annot = annFUN.org,
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282 mapping = geneuniverse, ID = "ensembl")
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283
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284 # Performing enrichment tests
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285 result <- runTest(mygodata, algorithm = option, statistic = "fisher") #nolint
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286 return(c(result, mygodata))
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287 }
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288
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289 args <- get_args()
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290
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291
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292 input_type <- args$inputtype
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293 input <- args$input
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294 onto <- args$ontology
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295 option <- args$option
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296 correction <- args$correction
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297 threshold <- as.numeric(args$threshold)
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298 text <- str2bool(args$textoutput)
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299 barplot <- "barplot" %in% unlist(strsplit(args$plot, ","))
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300 dotplot <- "dotplot" %in% unlist(strsplit(args$plot, ","))
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301 column <- as.numeric(gsub("c", "", args$column))
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302 geneuniverse <- args$geneuniverse
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303 header <- str2bool(args$header)
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304 background <- str2bool(args$background)
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305 if (background) {
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306 background_genes <- args$background_genes
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307 background_input_type <- args$background_input_type
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308 background_header <- str2bool(args$background_header)
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309 background_column <- as.numeric(gsub("c", "", args$background_column))
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310 }
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311
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312 #get input
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313 if (input_type == "copy_paste") {
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314 sample <- get_list_from_cp(input)
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315 } else if (input_type == "file") {
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316 tab <- read_file(input, header)
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317 sample <- trimws(unlist(strsplit(tab[, column], ";")))
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318 }
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319
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320 #check of ENS ids
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321 if (! any(check_ens_ids(sample))) {
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322 stop("no ensembl gene ids found in your ids list,
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323 please check your IDs in input or the selected column of your input file")
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324 }
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325
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326 #get input if background genes
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327 if (background) {
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328 if (background_input_type == "copy_paste") {
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329 background_sample <- get_list_from_cp(background_genes)
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330 } else if (background_input_type == "file") {
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331 background_tab <- read_file(background_genes, background_header)
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332 background_sample <- unique(trimws(unlist(
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333 strsplit(background_tab[, background_column], ";"))))
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334 }
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335 #check of ENS ids
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336 if (! any(check_ens_ids(background_sample))) {
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337 stop("no ensembl gene ids found in your background ids list,
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338 please check your IDs in input or the selected column of your input file")
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339 }
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340 } else {
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341 background_sample <- NULL
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342 }
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343
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344 # Launch enrichment analysis
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345 allresult <- suppressMessages(goenrichment(geneuniverse, sample,
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346 background_sample, onto))
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347 result <- allresult[1][[1]]
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348 mygodata <- allresult[2][[1]]
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349 if (!is.null(result)) {
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350 cut_result <- corrMultipleTesting(result, mygodata, correction, threshold)
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351 #Adjust the result with a multiple testing correction or not and with the
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352 #user, p-value cutoff
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353 }else {
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354 cut_result <- NULL
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355 }
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356
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357 createoutputs(result, cut_result, text, barplot, dotplot, onto)