Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.R @ 4:715002a394ec draft

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planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty
author proteore
date Fri, 23 Mar 2018 10:47:17 -0400
parents 58a8ddd58dde
children 781072a65600
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1 # Load necessary libraries
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2 library(org.Hs.eg.db)
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3 library(goProfiles)
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4
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5 # Read file and return file content as data.frame
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6 readfile = function(filename, header) {
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7 if (header == "true") {
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8 # Read only first line of the file as header:
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9 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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10 #Read the data of the files (skipping the first row)
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11 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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12 # Remove empty rows
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13 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
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14 #And assign the header to the data
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15 names(file) <- headers
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16 }
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17 else {
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18 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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19 # Remove empty rows
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20 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
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21 }
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22 return(file)
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23 }
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25 getprofile = function(ids, id_type, level, duplicate) {
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26 ####################################################################
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27 # Arguments
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28 # - ids: list of input IDs
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29 # - id_type: type of input IDs (UniProt/ENTREZID)
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30 # - level
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31 # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)
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32 ####################################################################
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33
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34 # Check if level is number
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35 if (! as.numeric(level) %% 1 == 0) {
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36 stop("Please enter an integer for level")
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37 }
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38 else {
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39 level = as.numeric(level)
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40 }
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41 #genes = as.vector(file[,ncol])
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42
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43 # Extract Gene Entrez ID
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44 if (id_type == "Entrez") {
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45 id = select(org.Hs.eg.db, ids, "ENTREZID", multiVals = "first")
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46 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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47 }
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48 else {
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49 genes_ids = c()
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50 id = select(org.Hs.eg.db, ids, "ENTREZID", "UNIPROT", multiVals = "first")
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51 if (duplicate == "TRUE") {
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52 id = unique(id)
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53 }
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54 print(id[[1]])
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55 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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56 # IDs that have NA ENTREZID
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57 NAs = id$UNIPROT[which(is.na(id$ENTREZID))]
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58 print("IDs unable to convert to ENTREZID: ")
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59 print(NAs)
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60 }
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61
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62 # Create basic profiles
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63 profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage="org.Hs.eg.db", empty.cats=F, ord=T, na.rm=T)
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64 profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage="org.Hs.eg.db", empty.cats=F, ord=T, na.rm=T)
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65 profile.MF = basicProfile(genes_ids, onto='MF', level=level, orgPackage="org.Hs.eg.db", empty.cats=F, ord=T, na.rm=T)
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66 profile.ALL = basicProfile(genes_ids, onto='ANY', level=level, orgPackage="org.Hs.eg.db", empty.cats=F, ord=T, na.rm=T)
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67
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68 # Print profile
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69 # printProfiles(profile)
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70
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71 return(c(profile.CC, profile.MF, profile.BP, profile.ALL))
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72 }
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73
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74 # Plot profiles to PNG
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75 plotPNG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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76 if (!is.null(profile.CC)) {
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77 png("profile.CC.png")
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78 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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79 dev.off()
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80 }
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81 if (!is.null(profile.BP)) {
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82 png("profile.BP.png")
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83 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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84 dev.off()
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85 }
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86 if (!is.null(profile.MF)) {
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87 png("profile.MF.png")
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88 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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89 dev.off()
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90 }
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91 if (!is.null(profile.ALL)) {
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92 png("profile.ALL.png")
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93 plotProfiles(profile.ALL, percentage=per, multiplePlots=T, aTitle=title)
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94 dev.off()
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95 }
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96 }
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97
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98 # Plot profiles to JPEG
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99 plotJPEG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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100 if (!is.null(profile.CC)) {
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101 jpeg("profile.CC.jpeg")
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102 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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103 dev.off()
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104 }
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105 if (!is.null(profile.BP)) {
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106 jpeg("profile.BP.jpeg")
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107 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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108 dev.off()
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109 }
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110 if (!is.null(profile.MF)) {
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111 jpeg("profile.MF.jpeg")
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112 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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113 dev.off()
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114 }
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115 if (!is.null(profile.ALL)) {
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116 jpeg("profile.ALL.jpeg")
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117 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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118 dev.off()
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119 }
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120 }
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121
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122 # Plot profiles to PDF
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123 plotPDF = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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124 if (!is.null(profile.CC)) {
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125 pdf("profile.CC.pdf")
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126 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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127 dev.off()
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128 }
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129 if (!is.null(profile.BP)) {
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130 pdf("profile.BP.pdf")
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131 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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132 dev.off()
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133 }
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134 if (!is.null(profile.MF)) {
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135 pdf("profile.MF.pdf")
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136 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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137 dev.off()
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138 }
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139 if (!is.null(profile.ALL)) {
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140 #print("all")
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141 pdf("profile.ALL.pdf")
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142 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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143 dev.off()
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144 }
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145 }
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146
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147 goprofiles = function() {
1
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148 args <- commandArgs(TRUE)
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149 if(length(args)<1) {
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150 args <- c("--help")
0
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151 }
1
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152
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153 # Help section
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154 if("--help" %in% args) {
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155 cat("Selection and Annotation HPA
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156 Arguments:
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157 --input_type: type of input (list of id or filename)
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158 --input: input
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159 --ncol: the column number which you would like to apply...
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160 --header: true/false if your file contains a header
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161 --id_type: the type of input IDs (UniProt/EntrezID)
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162 --onto_opt: ontology options
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163 --plot_opt: plot extension options (PDF/JPEG/PNG)
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164 --level: 1-3
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165 --per
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166 --title: title of the plot
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167 --duplicate: remove dupliate input IDs (true/false)
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168 --text_output: text output filename \n")
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169 q(save="no")
0
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170 }
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171
1
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172 # Parse arguments
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173 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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174 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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175 args <- as.list(as.character(argsDF$V2))
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176 names(args) <- argsDF$V1
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177
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178 input_type = args$input_type
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179 if (input_type == "text") {
4
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180 input = strsplit(args$input, "[ \t\n]+")[[1]]
1
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181 }
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182 else if (input_type == "file") {
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183 filename = args$input
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184 ncol = args$ncol
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185 # Check ncol
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186 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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187 stop("Please enter an integer for level")
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188 }
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189 else {
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190 ncol = as.numeric(gsub("c", "", ncol))
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191 }
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192 header = args$header
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193 # Get file content
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194 file = readfile(filename, header)
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195 # Extract Protein IDs list
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196 input = c()
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197 for (row in as.character(file[,ncol])) {
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198 input = c(input, strsplit(row, ";")[[1]][1])
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199 }
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200 }
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201 id_type = args$id_type
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202 ontoopt = strsplit(args$onto_opt, ",")[[1]]
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203 #print(ontoopt)
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204 #plotopt = strsplit(args[3], ",")
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205 plotopt = args$plot_opt
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206 level = args$level
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207 per = as.logical(args$per)
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208 title = args$title
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209 duplicate = args$duplicate
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210 text_output = args$text_output
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211
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212 profiles = getprofile(input, id_type, level, duplicate)
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213 profile.CC = profiles[1]
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214 #print(profile.CC)
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215 profile.MF = profiles[2]
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216 #print(profile.MF)
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217 profile.BP = profiles[3]
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218 #print(profile.BP)
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219 profile.ALL = profiles[-3:-1]
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220 #print(profile.ALL)
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221 #c(profile.ALL, profile.CC, profile.MF, profile.BP)
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222
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223 if ("CC" %in% ontoopt) {
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224 write.table(profile.CC, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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225 if (grepl("PNG", plotopt)) {
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226 plotPNG(profile.CC=profile.CC, per=per, title=title)
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227 }
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228 if (grepl("JPEG", plotopt)) {
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229 plotJPEG(profile.CC = profile.CC, per=per, title=title)
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230 }
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231 if (grepl("PDF", plotopt)) {
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232 plotPDF(profile.CC = profile.CC, per=per, title=title)
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233 }
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234 }
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235 if ("MF" %in% ontoopt) {
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236 write.table(profile.MF, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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237 if (grepl("PNG", plotopt)) {
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238 plotPNG(profile.MF = profile.MF, per=per, title=title)
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239 }
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240 if (grepl("JPEG", plotopt)) {
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241 plotJPEG(profile.MF = profile.MF, per=per, title=title)
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242 }
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243 if (grepl("PDF", plotopt)) {
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244 plotPDF(profile.MF = profile.MF, per=per, title=title)
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245 }
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246 }
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247 if ("BP" %in% ontoopt) {
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248 write.table(profile.BP, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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249 if (grepl("PNG", plotopt)) {
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250 plotPNG(profile.BP = profile.BP, per=per, title=title)
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251 }
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252 if (grepl("JPEG", plotopt)) {
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253 plotJPEG(profile.BP = profile.BP, per=per, title=title)
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254 }
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255 if (grepl("PDF", plotopt)) {
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256 plotPDF(profile.BP = profile.BP, per=per, title=title)
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257 }
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258 }
0
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259 }
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260
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261 goprofiles()