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annotate edger.R @ 12:a8305cf0c951 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
author iuc
date Thu, 21 Sep 2023 10:01:55 +0000
parents 6e53e565fc6a
children 0cb907a2a810
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9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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1 # This tool takes in a matrix of feature counts as well as gene annotations and
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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2 # outputs a table of top expressions as well as various plots for differential
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3 # expression analysis
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4 #
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5 # ARGS: htmlPath", "R", 1, "character" -Path to html file linking to other outputs
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6 # outPath", "o", 1, "character" -Path to folder to write all output to
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7 # filesPath", "j", 2, "character" -JSON list object if multiple files input
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8 # matrixPath", "m", 2, "character" -Path to count matrix
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9 # factFile", "f", 2, "character" -Path to factor information file
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10 # factInput", "i", 2, "character" -String containing factors if manually input
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11 # annoPath", "a", 2, "character" -Path to input containing gene annotations
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12 # contrastData", "C", 1, "character" -String containing contrasts of interest
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13 # cpmReq", "c", 2, "double" -Float specifying cpm requirement
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14 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement
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15 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement
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16 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output
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17 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output
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18 # lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement
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19 # pValReq", "p", 1, "double" -Float specifying the p-value requirement
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20 # pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method
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21 # normOpt", "n", 1, "character" -String specifying type of normalisation used
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22 # robOpt", "b", 0, "logical" -String specifying if robust options should be used
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23 # lrtOpt", "t", 0, "logical" -String specifying whether to perform LRT test instead
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24 #
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25 # OUT:
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26 # MDS Plot
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27 # BCV Plot
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28 # QL Plot
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29 # MD Plot
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30 # Expression Table
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31 # HTML file linking to the ouputs
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32 # Optional:
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33 # Normalised counts Table
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34 # RData file
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35 #
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36 # Author: Shian Su - registertonysu@gmail.com - Jan 2014
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37 # Modified by: Maria Doyle - Oct 2017 (some code taken from the DESeq2 wrapper)
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39 # Record starting time
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40 time_start <- as.character(Sys.time())
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42 # setup R error handling to go to stderr
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43 options(show.error.messages = FALSE, error = function() {
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44 cat(geterrmessage(), file = stderr())
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45 q("no", 1, FALSE)
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46 })
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48 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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49 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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51 # Load all required libraries
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52 library(methods, quietly = TRUE, warn.conflicts = FALSE)
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53 library(statmod, quietly = TRUE, warn.conflicts = FALSE)
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54 library(splines, quietly = TRUE, warn.conflicts = FALSE)
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55 library(edgeR, quietly = TRUE, warn.conflicts = FALSE)
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56 library(limma, quietly = TRUE, warn.conflicts = FALSE)
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57 library(scales, quietly = TRUE, warn.conflicts = FALSE)
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58 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
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60 ################################################################################
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61 ### Function Delcaration
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62 ################################################################################
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63 # Function to sanitise contrast equations so there are no whitespaces
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64 # surrounding the arithmetic operators, leading or trailing whitespace
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65 sanitise_equation <- function(equation) {
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66 equation <- gsub(" *[+] *", "+", equation)
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67 equation <- gsub(" *[-] *", "-", equation)
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68 equation <- gsub(" *[/] *", "/", equation)
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69 equation <- gsub(" *[*] *", "*", equation)
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70 equation <- gsub("^\\s+|\\s+$", "", equation)
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71 return(equation)
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72 }
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74 # Function to sanitise group information
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75 sanitise_groups <- function(string) {
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76 string <- gsub(" *[,] *", ",", string)
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77 string <- gsub("^\\s+|\\s+$", "", string)
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78 return(string)
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79 }
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81 # Function to change periods to whitespace in a string
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82 unmake_names <- function(string) {
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83 string <- gsub(".", " ", string, fixed = TRUE)
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84 return(string)
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85 }
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86
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87 # Generate output folder and paths
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88 make_out <- function(filename) {
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89 return(paste0(out_path, "/", filename))
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90 }
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91
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92 # Generating design information
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93 paste_listname <- function(string) {
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94 return(paste0("factors$", string))
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95 }
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96
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97 # Create cata function: default path set, default seperator empty and appending
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98 # true by default (Ripped straight from the cat function with altered argument
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99 # defaults)
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100 cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL,
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101 append = TRUE) {
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102 if (is.character(file)) {
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103 if (file == "") {
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104 file <- stdout()
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105 } else if (substring(file, 1L, 1L) == "|") {
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106 file <- pipe(substring(file, 2L), "w")
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107 on.exit(close(file))
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108 } else {
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109 file <- file(file, ifelse(append, "a", "w"))
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110 on.exit(close(file))
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111 }
8
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112 }
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113 .Internal(cat(list(...), file, sep, fill, labels, append))
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114 }
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115
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116 # Function to write code for html head and title
8
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117 html_head <- function(title) {
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118 cata("<head>\n")
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119 cata("<title>", title, "</title>\n")
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120 cata("</head>\n")
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121 }
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122
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123 # Function to write code for html links
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124 html_link <- function(address, label = address) {
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125 cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n")
0
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126 }
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127
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128 # Function to write code for html images
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129 html_image <- function(source, label = source, height = 600, width = 600) {
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130 cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height)
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131 cata("\" width=\"", width, "\"/>\n")
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132 }
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133
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134 # Function to write code for html list items
8
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135 list_item <- function(...) {
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136 cata("<li>", ..., "</li>\n")
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137 }
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138
8
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139 table_item <- function(...) {
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140 cata("<td>", ..., "</td>\n")
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141 }
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142
8
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143 table_head_item <- function(...) {
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144 cata("<th>", ..., "</th>\n")
0
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145 }
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146
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147 ################################################################################
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148 ### Input Processing
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149 ################################################################################
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150
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151 # Collect arguments from command line
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152 args <- commandArgs(trailingOnly = TRUE)
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153
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154 # Get options, using the spec as defined by the enclosed list.
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155 # Read the options from the default: commandArgs(TRUE).
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156 spec <- matrix(c(
8
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157 "htmlPath", "R", 1, "character",
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158 "outPath", "o", 1, "character",
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159 "filesPath", "j", 2, "character",
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160 "matrixPath", "m", 2, "character",
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161 "factFile", "f", 2, "character",
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162 "factInput", "i", 2, "character",
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163 "annoPath", "a", 2, "character",
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164 "contrastData", "C", 1, "character",
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165 "cpmReq", "c", 1, "double",
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166 "totReq", "y", 0, "logical",
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167 "cntReq", "z", 1, "integer",
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168 "sampleReq", "s", 1, "integer",
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169 "normCounts", "x", 0, "logical",
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170 "rdaOpt", "r", 0, "logical",
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171 "lfcReq", "l", 1, "double",
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172 "pValReq", "p", 1, "double",
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173 "pAdjOpt", "d", 1, "character",
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174 "normOpt", "n", 1, "character",
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175 "robOpt", "b", 0, "logical",
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176 "lrtOpt", "t", 0, "logical"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
177 ),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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diff changeset
178 byrow = TRUE, ncol = 4
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
179 )
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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180 opt <- getopt(spec)
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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181
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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182
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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diff changeset
183 if (is.null(opt$matrixPath) && is.null(opt$filesPath)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
184 cat("A counts matrix (or a set of counts files) is required.\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
185 q(status = 1)
0
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iuc
parents:
diff changeset
186 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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187
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
188 if (is.null(opt$cpmReq)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
189 filt_cpm <- FALSE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
190 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
191 filt_cpm <- TRUE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
192 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
193
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
194 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
195 filt_smpcount <- FALSE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
196 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
197 filt_smpcount <- TRUE
0
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iuc
parents:
diff changeset
198 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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199
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
200 if (is.null(opt$totReq)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
201 filt_totcount <- FALSE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
202 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
203 filt_totcount <- TRUE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
204 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
205
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
206 if (is.null(opt$lrtOpt)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
207 want_lrt <- FALSE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
208 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
209 want_lrt <- TRUE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
210 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
211
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
212 if (is.null(opt$rdaOpt)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
213 want_rda <- FALSE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
214 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
215 want_rda <- TRUE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
216 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
217
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
218 if (is.null(opt$annoPath)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
219 have_anno <- FALSE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
220 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
221 have_anno <- TRUE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
222 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
223
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
224 if (is.null(opt$normCounts)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
225 want_norm <- FALSE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
226 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
227 want_norm <- TRUE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
228 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
229
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
230 if (is.null(opt$robOpt)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
231 want_robust <- FALSE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
232 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
233 want_robust <- TRUE
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
234 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
235
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
236
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
237 if (!is.null(opt$filesPath)) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
238 # Process the separate count files (adapted from DESeq2 wrapper)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
239 library("rjson")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
240 parser <- newJSONParser()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
241 parser$addData(opt$filesPath)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
242 factor_list <- parser$getObject()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
243 factors <- sapply(factor_list, function(x) x[[1]])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
244 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
245 sampletable <- data.frame(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
246 sample = basename(filenames_in),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
247 filename = filenames_in,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
248 row.names = filenames_in,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
249 stringsAsFactors = FALSE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
250 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
251 for (factor in factor_list) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
252 factorname <- factor[[1]]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
253 sampletable[[factorname]] <- character(nrow(sampletable))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
254 lvls <- sapply(factor[[2]], function(x) names(x))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
255 for (i in seq_along(factor[[2]])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
256 files <- factor[[2]][[i]][[1]]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
257 sampletable[files, factorname] <- lvls[i]
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
258 }
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
259 sampletable[[factorname]] <- factor(sampletable[[factorname]], levels = lvls)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
260 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
261 rownames(sampletable) <- sampletable$sample
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
262 rem <- c("sample", "filename")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
263 factors <- sampletable[, !(names(sampletable) %in% rem), drop = FALSE]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
264
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
265 # read in count files and create single table
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
266 countfiles <- lapply(sampletable$filename, function(x) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
267 read.delim(x, row.names = 1)
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268 })
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269 counts <- do.call("cbind", countfiles)
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270 } else {
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271 # Process the single count matrix
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272 counts <- read.table(opt$matrixPath, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = FALSE)
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273 row.names(counts) <- counts[, 1]
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274 counts <- counts[, -1]
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275 countsrows <- nrow(counts)
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276
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277 # Process factors
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278 if (is.null(opt$factInput)) {
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279 factordata <- read.table(opt$factFile, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = TRUE)
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280 # check samples names match
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281 if (!any(factordata[, 1] %in% colnames(counts))) {
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282 stop("Sample IDs in factors file and count matrix don't match")
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283 }
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284 # order samples as in counts matrix
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285 factordata <- factordata[match(colnames(counts), factordata[, 1]), ]
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286 factors <- factordata[, -1, drop = FALSE]
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287 } else {
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288 factors <- unlist(strsplit(opt$factInput, "|", fixed = TRUE))
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289 factordata <- list()
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290 for (fact in factors) {
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291 newfact <- unlist(strsplit(fact, split = "::"))
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292 factordata <- rbind(factordata, newfact)
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293 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
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294
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295 # Set the row names to be the name of the factor and delete first row
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296 row.names(factordata) <- factordata[, 1]
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297 factordata <- factordata[, -1]
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298 factordata <- sapply(factordata, sanitise_groups)
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299 factordata <- sapply(factordata, strsplit, split = ",")
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300 factordata <- sapply(factordata, make.names)
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301 # Transform factor data into data frame of R factor objects
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302 factors <- data.frame(factordata)
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303 }
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304 }
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305
8
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306 # if annotation file provided
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307 if (have_anno) {
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308 geneanno <- read.table(opt$annoPath, header = TRUE, sep = "\t", quote = "", strip.white = TRUE, stringsAsFactors = FALSE)
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309 }
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310
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311 # Create output directory
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312 out_path <- opt$outPath
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313 dir.create(out_path, showWarnings = FALSE)
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314
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315 # Split up contrasts separated by comma into a vector then sanitise
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316 contrast_data <- unlist(strsplit(opt$contrastData, split = ","))
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317 contrast_data <- sanitise_equation(contrast_data)
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318 contrast_data <- gsub(" ", ".", contrast_data, fixed = TRUE)
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319
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320 bcv_pdf <- make_out("bcvplot.pdf")
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321 bcv_png <- make_out("bcvplot.png")
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322 ql_pdf <- make_out("qlplot.pdf")
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323 ql_png <- make_out("qlplot.png")
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324 mds_pdf <- character() # Initialise character vector
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325 mds_png <- character()
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326 for (i in seq_len(ncol(factors))) {
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327 mds_pdf[i] <- make_out(paste0("mdsplot_", names(factors)[i], ".pdf"))
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328 mds_png[i] <- make_out(paste0("mdsplot_", names(factors)[i], ".png"))
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329 }
8
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330 md_pdf <- character()
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331 md_png <- character()
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332 top_out <- character()
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333 for (i in seq_along(contrast_data)) {
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334 md_pdf[i] <- make_out(paste0("mdplot_", contrast_data[i], ".pdf"))
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335 md_png[i] <- make_out(paste0("mdplot_", contrast_data[i], ".png"))
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336 top_out[i] <- make_out(paste0("edgeR_", contrast_data[i], ".tsv"))
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337 } # Save output paths for each contrast as vectors
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338 norm_out <- make_out("edgeR_normcounts.tsv")
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339 rda_out <- make_out("edgeR_analysis.RData")
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340 session_out <- make_out("session_info.txt")
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341
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342 # Initialise data for html links and images, data frame with columns Label and
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343 # Link
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344 link_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
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345 image_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
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346
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347 # Initialise vectors for storage of up/down/neutral regulated counts
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348 up_count <- numeric()
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349 down_count <- numeric()
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350 flat_count <- numeric()
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351
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352 ################################################################################
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353 ### Data Processing
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
354 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
355
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
356 # Extract counts and annotation data
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
357 data <- list()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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358 data$counts <- counts
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
359 if (have_anno) {
3
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
360 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
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3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
361 annoord <- geneanno[match(row.names(counts), geneanno[, 1]), ]
3
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
362 data$genes <- annoord
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
363 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
364 data$genes <- data.frame(GeneID = row.names(counts))
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
365 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
366
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
367 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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368 # samples. Default is no filtering
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
369 prefilter_count <- nrow(data$counts)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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370
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
371 if (filt_cpm || filt_smpcount || filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
372 if (filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
373 keep <- rowSums(data$counts) >= opt$cntReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
374 } else if (filt_smpcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
375 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
376 } else if (filt_cpm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
377 keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
378 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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379
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
380 data$counts <- data$counts[keep, ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
381 data$genes <- data$genes[keep, , drop = FALSE]
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
382 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
383
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
384 postfilter_count <- nrow(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
385 filtered_count <- prefilter_count - postfilter_count
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
386
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
387 # Name rows of factors according to their sample
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
388 row.names(factors) <- names(data$counts)
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a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 9
diff changeset
389 factor_list <- names(factors)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
390
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
391 # Generating the DGEList object "data"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
392 samplenames <- colnames(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
393 genes <- data$genes
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
394 data <- DGEList(data$counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
395 colnames(data) <- samplenames
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
396 data$samples <- factors
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
397 data$genes <- genes
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
398
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
399
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
400
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
401 formula <- "~0"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
402 for (i in seq_along(factor_list)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
403 formula <- paste(formula, factor_list[i], sep = "+")
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
404 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
405
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
406 formula <- formula(formula)
12
a8305cf0c951 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents: 9
diff changeset
407 design <- model.matrix(formula, factors)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
408
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
409 for (i in seq_along(factor_list)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
410 colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
411 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
412
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
413 # Calculating normalising factor, estimating dispersion
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
414 data <- calcNormFactors(data, method = opt$normOpt)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
415
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
416 if (want_robust) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
417 data <- estimateDisp(data, design = design, robust = TRUE)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
418 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
419 data <- estimateDisp(data, design = design)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
420 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
421
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
422 # Generate contrasts information
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
423 contrasts <- makeContrasts(contrasts = contrast_data, levels = design)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
424
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
425 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
426 ### Data Output
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
427 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
428
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
429 # Plot MDS
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
430 labels <- names(counts)
3
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
431
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
432 # MDS plot
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
433 png(mds_png, width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
434 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
435 img_name <- paste0("MDS Plot_", names(factors)[1], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
436 img_addr <- paste0("mdsplot_", names(factors)[1], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
437 image_data[1, ] <- c(img_name, img_addr)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
438 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
439
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
440 pdf(mds_pdf)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
441 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
442 link_name <- paste0("MDS Plot_", names(factors)[1], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
443 link_addr <- paste0("mdsplot_", names(factors)[1], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
444 link_data[1, ] <- c(link_name, link_addr)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
445 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
446
3
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
447 # If additional factors create additional MDS plots coloured by factor
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
448 if (ncol(factors) > 1) {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
449 for (i in 2:ncol(factors)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
450 png(mds_png[i], width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
451 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
452 img_name <- paste0("MDS Plot_", names(factors)[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
453 img_addr <- paste0("mdsplot_", names(factors)[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
454 image_data <- rbind(image_data, c(img_name, img_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
455 invisible(dev.off())
3
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
456
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
457 pdf(mds_pdf[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
458 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
459 link_name <- paste0("MDS Plot_", names(factors)[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
460 link_addr <- paste0("mdsplot_", names(factors)[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
461 link_data <- rbind(link_data, c(link_name, link_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
462 invisible(dev.off())
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
463 }
3
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
464 }
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
465
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
466 # BCV Plot
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
467 png(bcv_png, width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
468 plotBCV(data, main = "BCV Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
469 img_name <- "BCV Plot"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
470 img_addr <- "bcvplot.png"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
471 image_data <- rbind(image_data, c(img_name, img_addr))
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
472 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
473
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
474 pdf(bcv_pdf)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
475 plotBCV(data, main = "BCV Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
476 link_name <- paste0("BCV Plot.pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
477 link_addr <- paste0("bcvplot.pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
478 link_data <- rbind(link_data, c(link_name, link_addr))
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
479 invisible(dev.off())
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
480
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
481 # Generate fit
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
482 if (want_lrt) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
483 fit <- glmFit(data, design)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
484 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
485 if (want_robust) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
486 fit <- glmQLFit(data, design, robust = TRUE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
487 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
488 fit <- glmQLFit(data, design)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
489 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
490
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
491 # Plot QL dispersions
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
492 png(ql_png, width = 600, height = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
493 plotQLDisp(fit, main = "QL Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
494 img_name <- "QL Plot"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
495 img_addr <- "qlplot.png"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
496 image_data <- rbind(image_data, c(img_name, img_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
497 invisible(dev.off())
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
498
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
499 pdf(ql_pdf)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
500 plotQLDisp(fit, main = "QL Plot")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
501 link_name <- "QL Plot.pdf"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
502 link_addr <- "qlplot.pdf"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
503 link_data <- rbind(link_data, c(link_name, link_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
504 invisible(dev.off())
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
505 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
506
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
507 # Save normalised counts (log2cpm)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
508 if (want_norm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
509 normalised_counts <- cpm(data, normalized.lib.sizes = TRUE, log = TRUE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
510 normalised_counts <- data.frame(data$genes, normalised_counts)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
511 write.table(normalised_counts, file = norm_out, row.names = FALSE, sep = "\t", quote = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
512 link_data <- rbind(link_data, c("edgeR_normcounts.tsv", "edgeR_normcounts.tsv"))
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
513 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
514
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
515
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
516 for (i in seq_along(contrast_data)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
517 if (want_lrt) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
518 res <- glmLRT(fit, contrast = contrasts[, i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
519 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
520 res <- glmQLFTest(fit, contrast = contrasts[, i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
521 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
522
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
523 status <- decideTestsDGE(res,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
524 adjust.method = opt$pAdjOpt, p.value = opt$pValReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
525 lfc = opt$lfcReq
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
526 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
527 sum_status <- summary(status)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
528
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
529 # Collect counts for differential expression
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
530 up_count[i] <- sum_status["Up", ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
531 down_count[i] <- sum_status["Down", ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
532 flat_count[i] <- sum_status["NotSig", ]
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
533
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
534 # Write top expressions table
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
535 top <- topTags(res, adjust.method = opt$pAdjOpt, n = Inf, sort.by = "PValue")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
536 write.table(top, file = top_out[i], row.names = FALSE, sep = "\t", quote = FALSE)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
537
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
538 link_name <- paste0("edgeR_", contrast_data[i], ".tsv")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
539 link_addr <- paste0("edgeR_", contrast_data[i], ".tsv")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
540 link_data <- rbind(link_data, c(link_name, link_addr))
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
541
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
542 # Plot MD (log ratios vs mean difference) using limma package
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
543 pdf(md_pdf[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
544 limma::plotMD(res,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
545 status = status,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
546 main = paste("MD Plot:", unmake_names(contrast_data[i])),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
547 hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
548 xlab = "Average Expression", ylab = "logFC"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
549 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
550
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
551 abline(h = 0, col = "grey", lty = 2)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
552
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
553 link_name <- paste0("MD Plot_", contrast_data[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
554 link_addr <- paste0("mdplot_", contrast_data[i], ".pdf")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
555 link_data <- rbind(link_data, c(link_name, link_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
556 invisible(dev.off())
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
557
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
558 png(md_png[i], height = 600, width = 600)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
559 limma::plotMD(res,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
560 status = status,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
561 main = paste("MD Plot:", unmake_names(contrast_data[i])),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
562 hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
563 xlab = "Average Expression", ylab = "logFC"
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
564 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
565
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
566 abline(h = 0, col = "grey", lty = 2)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
567
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
568 img_name <- paste0("MD Plot_", contrast_data[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
569 img_addr <- paste0("mdplot_", contrast_data[i], ".png")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
570 image_data <- rbind(image_data, c(img_name, img_addr))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
571 invisible(dev.off())
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
572 }
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
573 sig_diff <- data.frame(Up = up_count, Flat = flat_count, Down = down_count)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
574 row.names(sig_diff) <- contrast_data
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
575
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
576 # Save relevant items as rda object
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
577 if (want_rda) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
578 if (want_norm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
579 save(counts, data, status, normalised_counts, labels, factors, fit, res, top, contrasts, design,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
580 file = rda_out, ascii = TRUE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
581 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
582 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
583 save(counts, data, status, labels, factors, fit, res, top, contrasts, design,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
584 file = rda_out, ascii = TRUE
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
585 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
586 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
587 link_data <- rbind(link_data, c("edgeR_analysis.RData", "edgeR_analysis.RData"))
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
588 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
589
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
590 # Record session info
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
591 writeLines(capture.output(sessionInfo()), session_out)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
592 link_data <- rbind(link_data, c("Session Info", "session_info.txt"))
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
593
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
594 # Record ending time and calculate total run time
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
595 time_end <- as.character(Sys.time())
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
596 time_taken <- capture.output(round(difftime(time_end, time_start), digits = 3))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
597 time_taken <- gsub("Time difference of ", "", time_taken, fixed = TRUE)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
598
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
599 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
600 ### HTML Generation
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
601 ################################################################################
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
602
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
603 # Clear file
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
604 cat("", file = opt$htmlPath)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
605
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
606 cata("<html>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
607
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
608 cata("<body>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
609 cata("<h3>edgeR Analysis Output:</h3>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
610 cata("Links to PDF copies of plots are in 'Plots' section below.<br />\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
611
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
612 html_image(image_data$Link[1], image_data$Label[1])
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
613
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
614 for (i in 2:nrow(image_data)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
615 html_image(image_data$Link[i], image_data$Label[i])
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
616 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
617
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
618 cata("<h4>Differential Expression Counts:</h4>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
619
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
620 cata("<table border=\"1\" cellpadding=\"4\">\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
621 cata("<tr>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
622 table_item()
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
623 for (i in colnames(sig_diff)) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
624 table_head_item(i)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
625 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
626 cata("</tr>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
627 for (i in seq_len(nrow(sig_diff))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
628 cata("<tr>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
629 table_head_item(unmake_names(row.names(sig_diff)[i]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
630 for (j in seq_len(ncol(sig_diff))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
631 table_item(as.character(sig_diff[i, j]))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
632 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
633 cata("</tr>\n")
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
634 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
635 cata("</table>")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
636
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
637 cata("<h4>Plots:</h4>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
638 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
639 if (grepl(".pdf", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
640 html_link(link_data$Link[i], link_data$Label[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
641 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
642 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
643
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
644 cata("<h4>Tables:</h4>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
645 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
646 if (grepl(".tsv", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
647 html_link(link_data$Link[i], link_data$Label[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
648 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
649 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
650
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
651 if (want_rda) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
652 cata("<h4>R Data Objects:</h4>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
653 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
654 if (grepl(".RData", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
655 html_link(link_data$Link[i], link_data$Label[i])
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
656 }
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
657 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
658 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
659
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
660 cata("<p>Alt-click links to download file.</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
661 cata("<p>Click floppy disc icon associated history item to download ")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
662 cata("all files.</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
663 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
664
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
665 cata("<h4>Additional Information</h4>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
666 cata("<ul>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
667
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
668 if (filt_cpm || filt_smpcount || filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
669 if (filt_cpm) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
670 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
671 "Genes without more than", opt$cpmReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
672 "CPM in at least", opt$sampleReq, "samples are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
673 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
674 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
675 } else if (filt_smpcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
676 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
677 "Genes without more than", opt$cntReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
678 "counts in at least", opt$sampleReq, "samples are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
679 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
680 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
681 } else if (filt_totcount) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
682 temp_str <- paste(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
683 "Genes without more than", opt$cntReq,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
684 "counts, after summing counts for all samples, are insignificant",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
685 "and filtered out."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
686 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
687 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
688
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
689 list_item(temp_str)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
690 filter_prop <- round(filtered_count / prefilter_count * 100, digits = 2)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
691 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
692 filtered_count, " of ", prefilter_count, " (", filter_prop,
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
693 "%) genes were filtered out for low expression."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
694 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
695 list_item(temp_str)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
696 }
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
697 list_item(opt$normOpt, " was the method used to normalise library sizes.")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
698 if (want_lrt) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
699 list_item("The edgeR likelihood ratio test was used.")
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
700 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
701 if (want_robust) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
702 list_item("The edgeR quasi-likelihood test was used with robust settings (robust=TRUE with estimateDisp and glmQLFit).")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
703 } else {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
704 list_item("The edgeR quasi-likelihood test was used.")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
705 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
706 }
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
707 if (opt$pAdjOpt != "none") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
708 if (opt$pAdjOpt == "BH" || opt$pAdjOpt == "BY") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
709 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
710 "MD-Plot highlighted genes are significant at FDR ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
711 "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
712 "least ", opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
713 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
714 list_item(temp_str)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
715 } else if (opt$pAdjOpt == "holm") {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
716 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
717 "MD-Plot highlighted genes are significant at adjusted ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
718 "p-value of ", opt$pValReq, " by the Holm(1979) ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
719 "method, and exhibit log2-fold-change of at least ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
720 opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
721 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
722 list_item(temp_str)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
723 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
724 } else {
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
725 temp_str <- paste0(
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
726 "MD-Plot highlighted genes are significant at p-value ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
727 "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
728 "least ", opt$lfcReq, "."
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
729 )
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
730 list_item(temp_str)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
731 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
732 cata("</ul>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
733
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
734 cata("<h4>Summary of experimental data:</h4>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
735
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
736 cata("<p>*CHECK THAT SAMPLES ARE ASSOCIATED WITH CORRECT GROUP(S)*</p>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
737
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
738 cata("<table border=\"1\" cellpadding=\"3\">\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
739 cata("<tr>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
740 table_head_item("SampleID")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
741 table_head_item(names(factors)[1], " (Primary Factor)")
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
742
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
743 if (ncol(factors) > 1) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
744 for (i in names(factors)[2:length(names(factors))]) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
745 table_head_item(i)
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
746 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
747 cata("</tr>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
748 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
749
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
750 for (i in seq_len(nrow((factors)))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
751 cata("<tr>\n")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
752 table_head_item(row.names(factors)[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
753 for (j in seq_len(ncol(factors))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
754 table_item(as.character(unmake_names(factors[i, j])))
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
755 }
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
756 cata("</tr>\n")
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
757 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
758 cata("</table>")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
759
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
760 for (i in seq_len(nrow(link_data))) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
761 if (grepl("session_info", link_data$Link[i])) {
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
762 html_link(link_data$Link[i], link_data$Label[i])
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
763 }
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
764 }
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
765
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
766 cata("<table border=\"0\">\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
767 cata("<tr>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
768 table_item("Task started at:")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
769 table_item(time_start)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
770 cata("</tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
771 cata("<tr>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
772 table_item("Task ended at:")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
773 table_item(time_end)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
774 cata("</tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
775 cata("<tr>\n")
8
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
776 table_item("Task run time:")
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
777 table_item(time_taken)
0
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
778 cata("<tr>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
779 cata("</table>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
780
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
781 cata("</body>\n")
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
782 cata("</html>")