Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.R @ 0:d89c09253c8d draft

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planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
author proteore
date Sun, 26 Nov 2017 19:19:39 -0500
parents
children 1236ee08ccb8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 # Load necessary libraries
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2 library("org.Hs.eg.db", quietly=TRUE)
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3 library("goProfiles", quietly=TRUE)
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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 the first two lines of the files as data (without headers):
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9 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
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10 #print("header")
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11 #print(headers)
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12 # Create the headers names with the two (or more) first rows, sappy allows to make operations over the columns (in this case paste) - read more about sapply here :
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13 #headers_names <- sapply(headers, paste, collapse = "_")
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14 #print(headers_names)
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15 #Read the data of the files (skipping the first 2 rows):
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16 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
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17 #print(file[1,])
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18 #And assign the headers of step two to the data:
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19 names(file) <- headers
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20 }
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21 else {
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22 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
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23 }
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24 return(file)
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25 }
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26
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27 #filename = "/Users/LinCun/Documents/ProteoRE/usecase1/Check/HPA.Selection.134.txt"
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28 #test = readfile(filename)
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29 #str(test)
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30 #str(test$Gene.names)
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31 getprofile = function(ids, id_type, level, duplicate) {
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32 ####################################################################
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33 # Arguments
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34 # - ids: list of input IDs
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35 # - id_type: type of input IDs (UniProt/ENTREZID)
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36 # - level
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37 # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)
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38 ####################################################################
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39
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40 # Check if level is number
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41 if (! as.numeric(level) %% 1 == 0) {
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42 stop("Please enter an integer for level")
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43 }
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44 else {
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45 level = as.numeric(level)
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46 }
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47 #genes = as.vector(file[,ncol])
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48
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49 # Extract Gene Entrez ID
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50 if (id_type == "Entrez") {
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51 id = select(org.Hs.eg.db, ids, "ENTREZID", multiVals = "first")
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52 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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53 }
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54 else {
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55 genes_ids = c()
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56 id = select(org.Hs.eg.db, ids, "ENTREZID", "UNIPROT", multiVals = "first")
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57 if (duplicate == "TRUE") {
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58 id = unique(id)
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59 }
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60 print(id[[1]])
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61 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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62 # IDs that have NA ENTREZID
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63 NAs = id$UNIPROT[which(is.na(id$ENTREZID))]
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64 print("IDs unable to convert to ENTREZID: ")
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65 print(NAs)
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66 }
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67 #print(genes_ids)
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68 # Convert Protein IDs into entrez ids
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69
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70 # for (i in 1:length(id$UNIPROT)) {
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71 # print(i)
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72 # if (is.na(id[[2]][i])) {
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73 # print(id[[2]][i])
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74 # }
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75 # }
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76 # a = id[which(id$ENTREZID == "NA"),]
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77 # print(a)
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78 # print(a$UNIPROT)
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79 #print(id[[1]][which(is.na(id$ENTREZID))])
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80 #print(genes_ids)
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81 # for (gene in genes) {
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82 # #id = as.character(mget(gene, org.Hs.egALIAS2EG, ifnotfound = NA))
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83 # id = select(org.Hs.eg.db, genes, "ENTREZID", "UNIPROT")
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84 # print(id)
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85 # genes_ids = append(genes_ids, id$ENTREZID)
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86 # }
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87 #print(genes_ids)
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88
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89 # Create basic profiles
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90 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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91 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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92 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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93 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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94
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95 # Print profile
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96 # printProfiles(profile)
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97
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98 return(c(profile.CC, profile.MF, profile.BP, profile.ALL))
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99 }
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100
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101 # Plot profiles to PNG
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102 plotPNG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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103 if (!is.null(profile.CC)) {
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104 png("profile.CC.png")
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105 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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106 dev.off()
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107 }
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108 if (!is.null(profile.BP)) {
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109 png("profile.BP.png")
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110 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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111 dev.off()
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112 }
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113 if (!is.null(profile.MF)) {
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114 png("profile.MF.png")
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115 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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116 dev.off()
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117 }
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118 if (!is.null(profile.ALL)) {
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119 png("profile.ALL.png")
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120 plotProfiles(profile.ALL, percentage=per, multiplePlots=T, aTitle=title)
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121 dev.off()
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122 }
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123 }
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124
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125 # Plot profiles to JPEG
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126 plotJPEG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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127 if (!is.null(profile.CC)) {
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128 jpeg("profile.CC.jpeg")
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129 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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130 dev.off()
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131 }
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132 if (!is.null(profile.BP)) {
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133 jpeg("profile.BP.jpeg")
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134 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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135 dev.off()
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136 }
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137 if (!is.null(profile.MF)) {
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138 jpeg("profile.MF.jpeg")
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139 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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140 dev.off()
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141 }
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142 if (!is.null(profile.ALL)) {
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143 jpeg("profile.ALL.jpeg")
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144 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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145 dev.off()
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146 }
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147 }
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148
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149 # Plot profiles to PDF
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150 plotPDF = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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151 if (!is.null(profile.CC)) {
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152 pdf("profile.CC.pdf")
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153 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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154 dev.off()
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155 }
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156 if (!is.null(profile.BP)) {
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157 pdf("profile.BP.pdf")
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158 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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159 dev.off()
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160 }
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161 if (!is.null(profile.MF)) {
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162 pdf("profile.MF.pdf")
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163 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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164 dev.off()
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165 }
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166 if (!is.null(profile.ALL)) {
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167 #print("all")
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168 pdf("profile.ALL.pdf")
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169 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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170 dev.off()
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171 }
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172 }
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173
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174 goprofiles = function() {
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175 args = commandArgs(trailingOnly = TRUE)
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176 #print(args)
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177 # arguments: filename.R inputfile ncol "CC,MF,BP,ALL" "PNG,JPEG,PDF" level "TRUE"(percentage) "Title"
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178 if (length(args) != 9) {
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179 stop("Not enough/Too many arguments", call. = FALSE)
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180 }
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181 else {
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182 input_type = args[2]
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183 if (input_type == "text") {
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184 input = strsplit(args[1], "\\s+")[[1]]
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185 }
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186 else if (input_type == "file") {
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187 filename = strsplit(args[1], ",")[[1]][1]
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188 ncol = strsplit(args[1], ",")[[1]][2]
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189 # Check ncol
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190 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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191 stop("Please enter an integer for level")
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192 }
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193 else {
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194 ncol = as.numeric(gsub("c", "", ncol))
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195 }
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196 header = strsplit(args[1], ",")[[1]][3]
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197 # Get file content
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198 file = readfile(filename, header)
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199 # Extract Protein IDs list
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200 input = c()
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201 for (row in as.character(file[,ncol])) {
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202 input = c(input, strsplit(row, ";")[[1]][1])
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203 }
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204 }
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205 id_type = args[3]
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206 ontoopt = strsplit(args[4], ",")[[1]]
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207 #print(ontoopt)
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208 #plotopt = strsplit(args[3], ",")
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209 plotopt = args[5]
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210 level = args[6]
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211 per = as.logical(args[7])
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212 title = args[8]
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213 duplicate = args[9]
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214
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215 profiles = getprofile(input, id_type, level, duplicate)
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216 profile.CC = profiles[1]
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217 #print(profile.CC)
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218 profile.MF = profiles[2]
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219 #print(profile.MF)
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220 profile.BP = profiles[3]
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221 #print(profile.BP)
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222 profile.ALL = profiles[-3:-1]
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223 #print(profile.ALL)
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224 #c(profile.ALL, profile.CC, profile.MF, profile.BP)
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225 if ("CC" %in% ontoopt) {
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226 if (grepl("PNG", plotopt)) {
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227 plotPNG(profile.CC=profile.CC, per=per, title=title)
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228 }
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229 if (grepl("JPEG", plotopt)) {
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230 plotJPEG(profile.CC = profile.CC, per=per, title=title)
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231 }
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232 if (grepl("PDF", plotopt)) {
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233 plotPDF(profile.CC = profile.CC, per=per, title=title)
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234 }
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235 }
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236 if ("MF" %in% ontoopt) {
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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 if (grepl("PNG", plotopt)) {
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249 plotPNG(profile.BP = profile.BP, per=per, title=title)
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250 }
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251 if (grepl("JPEG", plotopt)) {
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252 plotJPEG(profile.BP = profile.BP, per=per, title=title)
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253 }
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254 if (grepl("PDF", plotopt)) {
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255 plotPDF(profile.BP = profile.BP, per=per, title=title)
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256 }
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257 }
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258
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259 #if (grepl("PNG", plotopt)) {
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260 # plotPNG(profile.ALL = profile.ALL, per=per, title=title)
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261 #}
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262 #if (grepl("JPEG", plotopt)) {
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263 # plotJPEG(profile.ALL = profile.ALL, per=per, title=title)
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264 #}
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265 #if (grepl("PDF", plotopt)) {
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266 # plotPDF(profile.ALL = profile.ALL, per=per, title=title)
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267 #}
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268 }
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269
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270 }
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271
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272 goprofiles()
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273
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274 #Rscript go.R ../proteinGroups_Maud.txt "1" "CC" "PDF" 2 "TRUE" "Title"