Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.R @ 1:1236ee08ccb8 draft

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planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
author proteore
date Fri, 16 Feb 2018 03:40:36 -0500
parents d89c09253c8d
children 58a8ddd58dde
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 line 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 #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)
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12 # Remove empty rows
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13 file <- file[!apply(is.na(file) | file == "", 1, all),]
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14 #And assign the headers of step two 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)
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19 }
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20 return(file)
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21 }
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22
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23 getprofile = function(ids, id_type, level, duplicate) {
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24 ####################################################################
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25 # Arguments
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26 # - ids: list of input IDs
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27 # - id_type: type of input IDs (UniProt/ENTREZID)
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28 # - level
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29 # - duplicate: if the duplicated IDs should be removed or not (TRUE/FALSE)
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30 ####################################################################
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31
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32 # Check if level is number
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33 if (! as.numeric(level) %% 1 == 0) {
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34 stop("Please enter an integer for level")
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35 }
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36 else {
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37 level = as.numeric(level)
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38 }
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39 #genes = as.vector(file[,ncol])
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40
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41 # Extract Gene Entrez ID
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42 if (id_type == "Entrez") {
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43 id = select(org.Hs.eg.db, ids, "ENTREZID", multiVals = "first")
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44 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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45 }
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46 else {
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47 genes_ids = c()
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48 id = select(org.Hs.eg.db, ids, "ENTREZID", "UNIPROT", multiVals = "first")
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49 if (duplicate == "TRUE") {
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50 id = unique(id)
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51 }
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52 print(id[[1]])
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53 genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
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54 # IDs that have NA ENTREZID
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55 NAs = id$UNIPROT[which(is.na(id$ENTREZID))]
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56 print("IDs unable to convert to ENTREZID: ")
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57 print(NAs)
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58 }
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59
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60 # Create basic profiles
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61 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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62 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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63 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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64 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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65
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66 # Print profile
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67 # printProfiles(profile)
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68
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69 return(c(profile.CC, profile.MF, profile.BP, profile.ALL))
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70 }
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71
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72 # Plot profiles to PNG
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73 plotPNG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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74 if (!is.null(profile.CC)) {
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75 png("profile.CC.png")
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76 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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77 dev.off()
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78 }
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79 if (!is.null(profile.BP)) {
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80 png("profile.BP.png")
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81 plotProfiles(profile.BP, percentage=per, multiplePlots=FALSE, aTitle=title)
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82 dev.off()
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83 }
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84 if (!is.null(profile.MF)) {
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85 png("profile.MF.png")
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86 plotProfiles(profile.MF, percentage=per, multiplePlots=FALSE, aTitle=title)
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87 dev.off()
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88 }
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89 if (!is.null(profile.ALL)) {
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90 png("profile.ALL.png")
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91 plotProfiles(profile.ALL, percentage=per, multiplePlots=T, aTitle=title)
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92 dev.off()
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93 }
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94 }
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95
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96 # Plot profiles to JPEG
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97 plotJPEG = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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98 if (!is.null(profile.CC)) {
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99 jpeg("profile.CC.jpeg")
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100 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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101 dev.off()
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102 }
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103 if (!is.null(profile.BP)) {
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104 jpeg("profile.BP.jpeg")
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105 plotProfiles(profile.BP, 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.MF)) {
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109 jpeg("profile.MF.jpeg")
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110 plotProfiles(profile.MF, 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.ALL)) {
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114 jpeg("profile.ALL.jpeg")
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115 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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116 dev.off()
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117 }
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118 }
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119
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120 # Plot profiles to PDF
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121 plotPDF = function(profile.CC = NULL, profile.BP = NULL, profile.MF = NULL, profile.ALL = NULL, per = TRUE, title = TRUE) {
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122 if (!is.null(profile.CC)) {
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123 pdf("profile.CC.pdf")
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124 plotProfiles(profile.CC, percentage=per, multiplePlots=FALSE, aTitle=title)
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125 dev.off()
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126 }
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127 if (!is.null(profile.BP)) {
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128 pdf("profile.BP.pdf")
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129 plotProfiles(profile.BP, 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.MF)) {
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133 pdf("profile.MF.pdf")
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134 plotProfiles(profile.MF, 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.ALL)) {
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138 #print("all")
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139 pdf("profile.ALL.pdf")
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140 plotProfiles(profile.ALL, percentage=per, multiplePlots=FALSE, aTitle=title)
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141 dev.off()
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142 }
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143 }
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144
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145 goprofiles = function() {
1
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146 args <- commandArgs(TRUE)
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147 if(length(args)<1) {
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148 args <- c("--help")
0
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149 }
1
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150
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151 # Help section
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152 if("--help" %in% args) {
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153 cat("Selection and Annotation HPA
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154 Arguments:
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155 --input_type: type of input (list of id or filename)
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156 --input: input
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157 --ncol: the column number which you would like to apply...
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158 --header: true/false if your file contains a header
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159 --id_type: the type of input IDs (UniProt/EntrezID)
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160 --onto_opt: ontology options
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161 --plot_opt: plot extension options (PDF/JPEG/PNG)
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162 --level: 1-3
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163 --per
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164 --title: title of the plot
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165 --duplicate: remove dupliate input IDs (true/false)
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166 --text_output: text output filename \n")
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167 q(save="no")
0
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168 }
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169
1
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170 # Parse arguments
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171 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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172 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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173 args <- as.list(as.character(argsDF$V2))
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174 names(args) <- argsDF$V1
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175
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176 input_type = args$input_type
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177 if (input_type == "text") {
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178 input = strsplit(args$input, " ")[[1]]
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179 }
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180 else if (input_type == "file") {
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181 filename = args$input
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182 ncol = args$ncol
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183 # Check ncol
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184 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
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185 stop("Please enter an integer for level")
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186 }
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187 else {
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188 ncol = as.numeric(gsub("c", "", ncol))
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189 }
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190 header = args$header
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191 # Get file content
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192 file = readfile(filename, header)
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193 # Extract Protein IDs list
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194 input = c()
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195 for (row in as.character(file[,ncol])) {
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196 input = c(input, strsplit(row, ";")[[1]][1])
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197 }
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198 }
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199 id_type = args$id_type
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200 ontoopt = strsplit(args$onto_opt, ",")[[1]]
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201 #print(ontoopt)
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202 #plotopt = strsplit(args[3], ",")
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203 plotopt = args$plot_opt
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204 level = args$level
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205 per = as.logical(args$per)
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206 title = args$title
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207 duplicate = args$duplicate
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208 text_output = args$text_output
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209
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210 profiles = getprofile(input, id_type, level, duplicate)
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211 profile.CC = profiles[1]
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212 #print(profile.CC)
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213 profile.MF = profiles[2]
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214 #print(profile.MF)
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215 profile.BP = profiles[3]
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216 #print(profile.BP)
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217 profile.ALL = profiles[-3:-1]
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218 #print(profile.ALL)
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219 #c(profile.ALL, profile.CC, profile.MF, profile.BP)
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220
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221 if ("CC" %in% ontoopt) {
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222 write.table(profile.CC, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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223 if (grepl("PNG", plotopt)) {
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224 plotPNG(profile.CC=profile.CC, per=per, title=title)
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225 }
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226 if (grepl("JPEG", plotopt)) {
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227 plotJPEG(profile.CC = profile.CC, per=per, title=title)
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228 }
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229 if (grepl("PDF", plotopt)) {
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230 plotPDF(profile.CC = profile.CC, per=per, title=title)
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231 }
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232 }
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233 if ("MF" %in% ontoopt) {
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234 write.table(profile.MF, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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235 if (grepl("PNG", plotopt)) {
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236 plotPNG(profile.MF = profile.MF, per=per, title=title)
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237 }
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238 if (grepl("JPEG", plotopt)) {
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239 plotJPEG(profile.MF = profile.MF, per=per, title=title)
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240 }
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241 if (grepl("PDF", plotopt)) {
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242 plotPDF(profile.MF = profile.MF, per=per, title=title)
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243 }
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244 }
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245 if ("BP" %in% ontoopt) {
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246 write.table(profile.BP, text_output, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
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247 if (grepl("PNG", plotopt)) {
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248 plotPNG(profile.BP = profile.BP, per=per, title=title)
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249 }
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250 if (grepl("JPEG", plotopt)) {
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251 plotJPEG(profile.BP = profile.BP, per=per, title=title)
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252 }
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253 if (grepl("PDF", plotopt)) {
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254 plotPDF(profile.BP = profile.BP, per=per, title=title)
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255 }
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256 }
0
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257 }
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258
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259 goprofiles()