Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.R @ 5:781072a65600 draft

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author proteore
date Wed, 19 Sep 2018 05:49:06 -0400
parents 715002a394ec
children 6afe8166a9a4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 # Load necessary libraries
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2 library(goProfiles,quietly = TRUE)
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4 # Read file and return file content as data.frame
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5 readfile = function(filename, header) {
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6 if (header == "true") {
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7 # Read only first line of the file as header:
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8 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
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9 #Read the data of the files (skipping the first row)
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10 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
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11 # Remove empty rows
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12 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
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13 #And assign the header to the data
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14 names(file) <- headers
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15 }
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16 else {
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17 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
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18 # Remove empty rows
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19 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
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20 }
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21 return(file)
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22 }
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23
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24 check_ids <- function(vector,type) {
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25 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})$"
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26 entrez_id = "^'[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
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27 if (type == "Entrez"){
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28 return(grepl(entrez_id,vector))
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29 } else if (type == "UniProt") {
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30 return(grepl(uniprot_pattern,vector))
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31 }
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32 }
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34 getprofile = function(ids, id_type, level, duplicate,species) {
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35 ####################################################################
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36 # Arguments
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37 # - ids: list of input IDs
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38 # - id_type: type of input IDs (UniProt/ENTREZID)
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39 # - level
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40 # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)
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41 # - species
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42 ####################################################################
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43
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44 library(species, character.only = TRUE, quietly = TRUE)
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45
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46 if (species=="org.Hs.eg.db"){
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47 package=org.Hs.eg.db
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48 } else if (species=="org.Mm.eg.db"){
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49 package=org.Mm.eg.db
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50 }
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53
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54 # Check if level is number
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55 if (! as.numeric(level) %% 1 == 0) {
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56 stop("Please enter an integer for level")
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57 } else {
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58 level = as.numeric(level)
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59 }
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60 #genes = as.vector(file[,ncol])
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61
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62 # Extract Gene Entrez ID
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63 if (id_type == "Entrez") {
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64 id = select(package, ids, "ENTREZID", multiVals = "first")
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65 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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66 } else {
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67 genes_ids = c()
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68 id = select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first")
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69 if (duplicate == "TRUE") {
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70 id = unique(id)
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71 }
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72 print(id[[1]])
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73 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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74 # IDs that have NA ENTREZID
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75 NAs = id$UNIPROT[which(is.na(id$ENTREZID))]
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76 print("IDs unable to convert to ENTREZID: ")
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77 print(NAs)
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78 }
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79
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80 # Create basic profiles
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81 profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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82 profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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83 profile.MF = basicProfile(genes_ids, onto='MF', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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84 profile.ALL = basicProfile(genes_ids, onto='ANY', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
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85
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86 # Print profile
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87 # printProfiles(profile)
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88
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89 return(c(profile.CC, profile.MF, profile.BP, profile.ALL))
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90 }
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91
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92 # Plot profiles to PNG
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93 plotPNG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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94 if (!is.null(profile.CC)) {
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95 png("profile.CC.png")
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96 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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97 dev.off()
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98 }
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99 if (!is.null(profile.BP)) {
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100 png("profile.BP.png")
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101 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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102 dev.off()
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103 }
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104 if (!is.null(profile.MF)) {
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105 png("profile.MF.png")
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106 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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107 dev.off()
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108 }
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109 if (!is.null(profile.ALL)) {
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110 png("profile.ALL.png")
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111 plotProfiles(profile.ALL, percentage=per, multiplePlots=T, aTitle=title)
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112 dev.off()
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113 }
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114 }
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115
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116 # Plot profiles to JPEG
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117 plotJPEG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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118 if (!is.null(profile.CC)) {
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119 jpeg("profile.CC.jpeg")
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120 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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121 dev.off()
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122 }
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123 if (!is.null(profile.BP)) {
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124 jpeg("profile.BP.jpeg")
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125 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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126 dev.off()
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127 }
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128 if (!is.null(profile.MF)) {
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129 jpeg("profile.MF.jpeg")
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130 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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131 dev.off()
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132 }
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133 if (!is.null(profile.ALL)) {
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134 jpeg("profile.ALL.jpeg")
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135 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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136 dev.off()
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137 }
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138 }
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139
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140 # Plot profiles to PDF
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141 plotPDF = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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142 if (!is.null(profile.CC)) {
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143 pdf("profile.CC.pdf")
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144 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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145 dev.off()
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146 }
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147 if (!is.null(profile.BP)) {
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148 pdf("profile.BP.pdf")
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149 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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150 dev.off()
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151 }
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152 if (!is.null(profile.MF)) {
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153 pdf("profile.MF.pdf")
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154 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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155 dev.off()
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156 }
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157 if (!is.null(profile.ALL)) {
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158 #print("all")
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159 pdf("profile.ALL.pdf")
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160 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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161 dev.off()
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162 }
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163 }
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164
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165 goprofiles = function() {
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166 args <- commandArgs(TRUE)
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167 if(length(args)<1) {
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168 args <- c("--help")
0
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169 }
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170
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171 # Help section
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172 if("--help" %in% args) {
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173 cat("Selection and Annotation HPA
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174 Arguments:
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175 --input_type: type of input (list of id or filename)
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176 --input: input
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177 --ncol: the column number which you would like to apply...
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178 --header: true/false if your file contains a header
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179 --id_type: the type of input IDs (UniProt/EntrezID)
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180 --onto_opt: ontology options
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181 --plot_opt: plot extension options (PDF/JPEG/PNG)
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182 --level: 1-3
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183 --per
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184 --title: title of the plot
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185 --duplicate: remove dupliate input IDs (true/false)
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186 --text_output: text output filename \n
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187 --species")
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188 q(save="no")
0
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189 }
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190
1
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191 # Parse arguments
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192 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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193 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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194 args <- as.list(as.character(argsDF$V2))
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195 names(args) <- argsDF$V1
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196
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197 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
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198 #load("/home/dchristiany/proteore_project/ProteoRE/tools/goprofiles/args.Rda")
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199
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200 id_type = args$id_type
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201 input_type = args$input_type
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202 if (input_type == "text") {
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203 input = strsplit(args$input, "[ \t\n]+")[[1]]
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204 } else if (input_type == "file") {
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205 filename = args$input
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206 ncol = args$ncol
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207 # Check ncol
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208 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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209 stop("Please enter an integer for level")
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210 } else {
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211 ncol = as.numeric(gsub("c", "", ncol))
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212 }
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213 header = args$header
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214 # Get file content
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215 file = readfile(filename, header)
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216 # Extract Protein IDs list
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217 input = c()
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218 for (row in as.character(file[,ncol])) {
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219 input = c(input, strsplit(row, ";")[[1]][1])
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220 }
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221 }
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222
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223 if (! any(check_ids(input,id_type))){
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224 stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file"))
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225 }
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226
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227 ontoopt = strsplit(args$onto_opt, ",")[[1]]
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228 #print(ontoopt)
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229 #plotopt = strsplit(args[3], ",")
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230 plotopt = args$plot_opt
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231 level = args$level
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232 per = as.logical(args$per)
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233 title = args$title
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234 duplicate = args$duplicate
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235 text_output = args$text_output
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236 species=args$species
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237
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238 profiles = getprofile(input, id_type, level, duplicate,species)
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239 profile.CC = profiles[1]
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240 #print(profile.CC)
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241 profile.MF = profiles[2]
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242 #print(profile.MF)
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243 profile.BP = profiles[3]
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244 #print(profile.BP)
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245 profile.ALL = profiles[-3:-1]
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246 #print(profile.ALL)
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247 #c(profile.ALL, profile.CC, profile.MF, profile.BP)
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248
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249 if ("CC" %in% ontoopt) {
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250 write.table(profile.CC, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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251 if (grepl("PNG", plotopt)) {
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252 plotPNG(profile.CC=profile.CC, per=per, title=title)
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253 }
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254 if (grepl("JPEG", plotopt)) {
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255 plotJPEG(profile.CC = profile.CC, per=per, title=title)
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256 }
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257 if (grepl("PDF", plotopt)) {
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258 plotPDF(profile.CC = profile.CC, per=per, title=title)
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259 }
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260 }
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261 if ("MF" %in% ontoopt) {
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262 write.table(profile.MF, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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263 if (grepl("PNG", plotopt)) {
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264 plotPNG(profile.MF = profile.MF, per=per, title=title)
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265 }
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266 if (grepl("JPEG", plotopt)) {
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267 plotJPEG(profile.MF = profile.MF, per=per, title=title)
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268 }
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269 if (grepl("PDF", plotopt)) {
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270 plotPDF(profile.MF = profile.MF, per=per, title=title)
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271 }
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272 }
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273 if ("BP" %in% ontoopt) {
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274 write.table(profile.BP, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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275 if (grepl("PNG", plotopt)) {
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276 plotPNG(profile.BP = profile.BP, per=per, title=title)
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277 }
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278 if (grepl("JPEG", plotopt)) {
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279 plotJPEG(profile.BP = profile.BP, per=per, title=title)
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280 }
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281 if (grepl("PDF", plotopt)) {
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282 plotPDF(profile.BP = profile.BP, per=per, title=title)
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283 }
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284 }
0
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285 }
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286
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287 goprofiles()