Mercurial > repos > proteore > proteore_go_terms_profiles_comparison

annotate GO_prof_comp.R @ 0:a0ea9e00bd66 draft

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planemo upload commit e5e4a3efd1cb1498724c0e93f8ec9606d0ed3045-dirty
author proteore
date Thu, 28 Feb 2019 05:53:47 -0500
parents
children 67a4f68f1c1c
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1 options(warn=-1) #TURN OFF WARNINGS !!!!!!
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2 suppressMessages(library(clusterProfiler,quietly = TRUE))
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3
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4 #return the number of character from the longest description found (from the 10 first)
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5 max_str_length_10_first <- function(vector){
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6 vector <- as.vector(vector)
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7 nb_description = length(vector)
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8 if (nb_description >= 10){nb_description=10}
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9 return(max(nchar(vector[1:nb_description])))
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10 }
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11
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12 str2bool <- function(x){
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13 if (any(is.element(c("t","true"),tolower(x)))){
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14 return (TRUE)
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15 }else if (any(is.element(c("f","false"),tolower(x)))){
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16 return (FALSE)
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17 }else{
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18 return(NULL)
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19 }
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20 }
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21
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22 get_args <- function(){
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23
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24 ## Collect arguments
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25 args <- commandArgs(TRUE)
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26
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27 ## Default setting when no arguments passed
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28 if(length(args) < 1) {
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29 args <- c("--help")
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30 }
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31
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32 ## Help section
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33 if("--help" %in% args) {
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34 cat("Selection and Annotation HPA
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35 Arguments:
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36 --inputtype1: type of input (list of id or filename)
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37 --inputtype2: type of input (list of id or filename)
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38 --input1: input1
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39 --input2: input2
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40 --column1: the column number which you would like to apply...
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41 --column2: the column number which you would like to apply...
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42 --header1: true/false if your file contains a header
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43 --header2: true/false if your file contains a header
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44 --ont: ontology to use
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45 --lev: ontology level
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46 --org: organism db package
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47 --list_name1: name of the first list
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48 --list_name2: name of the second list \n")
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49
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50 q(save="no")
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51 }
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52
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53 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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54 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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55 args <- as.list(as.character(argsDF$V2))
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56 names(args) <- argsDF$V1
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57
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58 return(args)
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59 }
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60
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61 get_ids=function(inputtype, input, ncol, header) {
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62
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63 if (inputtype == "text") {
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64 ids = strsplit(input, "[ \t\n]+")[[1]]
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65 } else if (inputtype == "file") {
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66 header=str2bool(header)
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67 ncol=get_cols(ncol)
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68 csv = read.csv(input,header=header, sep="\t", as.is=T)
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69 ids=csv[,ncol]
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70 }
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71
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72 ids = unlist(strsplit(ids,";"))
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73 ids = ids[which(!is.na(ids))]
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74
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75 return(ids)
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76 }
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77
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78 str2bool <- function(x){
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79 if (any(is.element(c("t","true"),tolower(x)))){
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80 return (TRUE)
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81 }else if (any(is.element(c("f","false"),tolower(x)))){
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82 return (FALSE)
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83 }else{
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84 return(NULL)
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85 }
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86 }
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87
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88 check_ids <- function(vector,type) {
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89 uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
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90 entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
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91 if (type == "entrez")
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92 return(grepl(entrez_id,vector))
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93 else if (type == "uniprot") {
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94 return(grepl(uniprot_pattern,vector))
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95 }
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96 }
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97
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98 make_dotplot<-function(res.cmp,ontology) {
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99
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100 res.cmp@compareClusterResult$Description <- sapply(as.vector(res.cmp@compareClusterResult$Description), function(x) {ifelse(nchar(x)>50, substr(x,1,50),x)},USE.NAMES = FALSE)
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101 output_path= paste("GO_profiles_comp_",ontology,".png",sep="")
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102 png(output_path,height = 720, width = 600)
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103 p <- dotplot(res.cmp, showCategory=30)
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104 print(p)
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105 dev.off()
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106 }
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107
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108 get_cols <-function(input_cols) {
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109 input_cols <- gsub("c","",gsub("C","",gsub(" ","",input_cols)))
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110 if (grepl(":",input_cols)) {
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111 first_col=unlist(strsplit(input_cols,":"))[1]
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112 last_col=unlist(strsplit(input_cols,":"))[2]
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113 cols=first_col:last_col
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114 } else {
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115 cols = as.integer(unlist(strsplit(input_cols,",")))
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116 }
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117 return(cols)
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118 }
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119
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120 #to check
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121 cmp.GO <- function(l,fun="groupGO",orgdb, ontology, level=3, readable=TRUE) {
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122 cmpGO<-compareCluster(geneClusters = l,
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123 fun=fun,
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124 OrgDb = orgdb,
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125 ont=ontology,
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126 level=level,
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127 readable=TRUE)
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128
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129 return(cmpGO)
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130 }
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131
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132 check_ids <- function(vector,type) {
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133 uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
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134 entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
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135 if (type == "entrez")
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136 return(grepl(entrez_id,vector))
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137 else if (type == "uniprot") {
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138 return(grepl(uniprot_pattern,vector))
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139 }
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140 }
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141
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142 main = function() {
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143
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144 #to get the args of the command line
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145 args=get_args()
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146
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147 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/GO_terms_profiles_comparison/args.rda")
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148 #load("/home/dchristiany/proteore_project/ProteoRE/tools/GO_terms_profiles_comparison/args.rda")
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149
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150 ids1<-get_ids(args$inputtype1, args$input1, args$column1, args$header1)
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151 ids2<-get_ids(args$inputtype2, args$input2, args$column2, args$header2)
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152 ont = strsplit(args$ont, ",")[[1]]
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153 lev=as.integer(args$lev)
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154 org=args$org
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155
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156 #load annot package
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157 suppressMessages(library(args$org, character.only = TRUE, quietly = TRUE))
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158
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159 # Extract OrgDb
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160 if (args$org=="org.Hs.eg.db") {
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161 orgdb<-org.Hs.eg.db
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162 } else if (args$org=="org.Mm.eg.db") {
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163 orgdb<-org.Mm.eg.db
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164 } else if (args$org=="org.Rn.eg.db") {
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165 orgdb<-org.Rn.eg.db
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166 }
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167
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168 for(ontology in ont) {
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169 liste = list("l1"=ids1,"l2"=ids2)
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170 names(liste) = c(args$list_name1,args$list_name2)
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171 res.cmp<-cmp.GO(l=liste,fun="groupGO",orgdb, ontology, level=lev, readable=TRUE)
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172 make_dotplot(res.cmp,ontology)
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173 output_path = paste("GO_profiles_comp_",ontology,".tsv",sep="")
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174 write.table(res.cmp@compareClusterResult, output_path, sep="\t", row.names=F, quote=F)
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175 }
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176
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177 } #end main
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178
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179 main()
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180