Mercurial > repos > iuc > limma_voom

annotate limma_voom.R @ 10:e26047c4562d draft

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author iuc
date Fri, 08 Jun 2018 02:20:16 -0400
parents 4255881bebb1
children 7e8af58c8052
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1 # This tool takes in a matrix of feature counts as well as gene annotations and
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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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 # trend", "t", 1, "double" -Float for prior.count if limma-trend is used instead of voom
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24 # weightOpt", "w", 0, "logical" -String specifying if voomWithQualityWeights should be used
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25 # topgenes", "G", 1, "integer" -Integer specifying no. of genes to highlight in volcano and heatmap
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26 # treatOpt", "T", 0, "logical" -String specifying if TREAT function should be used
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27 # plots, "P", 1, "character" -String specifying additional plots to be created
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28 #
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29 # OUT:
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30 # Density Plots (if filtering)
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31 # Box Plots (if normalising)
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32 # MDS Plot
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33 # Voom/SA plot
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34 # MD Plot
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35 # Volcano Plot
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36 # Heatmap
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37 # Expression Table
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38 # HTML file linking to the ouputs
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39 # Optional:
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40 # Normalised counts Table
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41 # RData file
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42 #
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43 #
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44 # Author: Shian Su - registertonysu@gmail.com - Jan 2014
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45 # Modified by: Maria Doyle - Jun 2017, Jan 2018, May 2018
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47 # Record starting time
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48 timeStart <- as.character(Sys.time())
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50 # Load all required libraries
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51 library(methods, quietly=TRUE, warn.conflicts=FALSE)
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52 library(statmod, quietly=TRUE, warn.conflicts=FALSE)
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53 library(splines, quietly=TRUE, warn.conflicts=FALSE)
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54 library(edgeR, quietly=TRUE, warn.conflicts=FALSE)
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55 library(limma, quietly=TRUE, warn.conflicts=FALSE)
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56 library(scales, quietly=TRUE, warn.conflicts=FALSE)
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57 library(getopt, quietly=TRUE, warn.conflicts=FALSE)
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58 library(gplots, quietly=TRUE, warn.conflicts=FALSE)
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60 ################################################################################
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61 ### Function Declaration
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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 sanitiseEquation <- 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+$", "", equation)
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71 return(equation)
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72 }
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74 # Function to sanitise group information
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75 sanitiseGroups <- function(string) {
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76 string <- gsub(" *[,] *", ",", string)
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77 string <- gsub("^\\s+|\\s+$", "", 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 makeOut <- function(filename) {
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89 return(paste0(opt$outPath, "/", filename))
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90 }
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91
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92 # Generating design information
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93 pasteListName <- function(string) {
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94 return(paste0("factors$", 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 }
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109 else {
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110 file <- file(file, ifelse(append, "a", "w"))
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111 on.exit(close(file))
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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
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117 HtmlHead <- function(title) {
3
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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 HtmlLink <- function(address, label=address) {
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125 cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n")
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126 }
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127
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128 # Function to write code for html images
8
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129 HtmlImage <- function(source, label=source, height=500, width=500) {
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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
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135 ListItem <- function(...) {
3
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136 cata("<li>", ..., "</li>\n")
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137 }
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138
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139 TableItem <- function(...) {
3
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140 cata("<td>", ..., "</td>\n")
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141 }
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142
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143 TableHeadItem <- function(...) {
3
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144 cata("<th>", ..., "</th>\n")
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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
3
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151 # Collect arguments from command line
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152 args <- commandArgs(trailingOnly=TRUE)
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153
3
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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(
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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 "trend", "t", 1, "double",
6
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177 "weightOpt", "w", 0, "logical",
7
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178 "topgenes", "G", 1, "integer",
8
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179 "treatOpt", "T", 0, "logical",
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180 "plots", "P", 1, "character"),
3
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181 byrow=TRUE, ncol=4)
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182 opt <- getopt(spec)
0
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183
1
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184
3
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185 if (is.null(opt$matrixPath) & is.null(opt$filesPath)) {
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186 cat("A counts matrix (or a set of counts files) is required.\n")
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187 q(status=1)
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188 }
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189
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190 if (is.null(opt$cpmReq)) {
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191 filtCPM <- FALSE
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192 } else {
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193 filtCPM <- TRUE
1
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194 }
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195
3
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196 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) {
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197 filtSmpCount <- FALSE
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198 } else {
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199 filtSmpCount <- TRUE
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200 }
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201
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202 if (is.null(opt$totReq)) {
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203 filtTotCount <- FALSE
0
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204 } else {
3
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205 filtTotCount <- TRUE
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206 }
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207
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208 if (is.null(opt$rdaOpt)) {
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209 wantRda <- FALSE
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210 } else {
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211 wantRda <- TRUE
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212 }
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213
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214 if (is.null(opt$annoPath)) {
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diff changeset
215 haveAnno <- FALSE
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216 } else {
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217 haveAnno <- TRUE
0
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218 }
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219
3
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220 if (is.null(opt$normCounts)) {
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221 wantNorm <- FALSE
0
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222 } else {
3
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diff changeset
223 wantNorm <- TRUE
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224 }
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225
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226 if (is.null(opt$robOpt)) {
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diff changeset
227 wantRobust <- FALSE
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228 } else {
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229 wantRobust <- TRUE
0
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230 }
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231
3
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232 if (is.null(opt$weightOpt)) {
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233 wantWeight <- FALSE
0
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234 } else {
3
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235 wantWeight <- TRUE
0
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236 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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237
3
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238 if (is.null(opt$trend)) {
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239 wantTrend <- FALSE
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240 deMethod <- "limma-voom"
1
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241 } else {
3
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242 wantTrend <- TRUE
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243 deMethod <- "limma-trend"
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244 priorCount <- opt$trend
1
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245 }
0
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246
6
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247 if (is.null(opt$treatOpt)) {
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diff changeset
248 wantTreat <- FALSE
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249 } else {
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diff changeset
250 wantTreat <- TRUE
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251 }
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252
0
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253
3
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254 if (!is.null(opt$filesPath)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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255 # Process the separate count files (adapted from DESeq2 wrapper)
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diff changeset
256 library("rjson")
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257 parser <- newJSONParser()
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258 parser$addData(opt$filesPath)
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259 factorList <- parser$getObject()
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260 factors <- sapply(factorList, function(x) x[[1]])
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261 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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262 sampleTable <- data.frame(sample=basename(filenamesIn),
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263 filename=filenamesIn,
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diff changeset
264 row.names=filenamesIn,
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265 stringsAsFactors=FALSE)
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266 for (factor in factorList) {
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267 factorName <- factor[[1]]
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268 sampleTable[[factorName]] <- character(nrow(sampleTable))
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269 lvls <- sapply(factor[[2]], function(x) names(x))
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270 for (i in seq_along(factor[[2]])) {
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271 files <- factor[[2]][[i]][[1]]
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272 sampleTable[files,factorName] <- lvls[i]
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273 }
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274 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls)
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275 }
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276 rownames(sampleTable) <- sampleTable$sample
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277 rem <- c("sample","filename")
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278 factors <- sampleTable[, !(names(sampleTable) %in% rem), drop=FALSE]
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279
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280 #read in count files and create single table
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281 countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)})
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282 counts <- do.call("cbind", countfiles)
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283
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284 } else {
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285 # Process the single count matrix
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286 counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE)
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287 row.names(counts) <- counts[, 1]
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288 counts <- counts[ , -1]
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289 countsRows <- nrow(counts)
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290
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291 # Process factors
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292 if (is.null(opt$factInput)) {
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293 factorData <- read.table(opt$factFile, header=TRUE, sep="\t")
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294 factors <- factorData[, -1, drop=FALSE]
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295 } else {
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296 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))
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297 factorData <- list()
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298 for (fact in factors) {
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299 newFact <- unlist(strsplit(fact, split="::"))
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300 factorData <- rbind(factorData, newFact)
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301 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
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302
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303 # Set the row names to be the name of the factor and delete first row
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304 row.names(factorData) <- factorData[, 1]
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305 factorData <- factorData[, -1]
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306 factorData <- sapply(factorData, sanitiseGroups)
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307 factorData <- sapply(factorData, strsplit, split=",")
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308 factorData <- sapply(factorData, make.names)
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309 # Transform factor data into data frame of R factor objects
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310 factors <- data.frame(factorData)
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311 }
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312 }
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313
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314 # if annotation file provided
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315 if (haveAnno) {
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316 geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", stringsAsFactors=FALSE)
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317 }
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318
0
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319 #Create output directory
3
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320 dir.create(opt$outPath, showWarnings=FALSE)
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321
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322 # Split up contrasts seperated by comma into a vector then sanitise
3
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323 contrastData <- unlist(strsplit(opt$contrastData, split=","))
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324 contrastData <- sanitiseEquation(contrastData)
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325 contrastData <- gsub(" ", ".", contrastData, fixed=TRUE)
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326
8
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327 plots <- character()
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328 if (!is.null(opt$plots)) {
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329 plots <- unlist(strsplit(opt$plots, split=","))
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330 }
3
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331
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332 denOutPng <- makeOut("densityplots.png")
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333 denOutPdf <- makeOut("densityplots.pdf")
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334 cpmOutPdf <- makeOut("cpmplots.pdf")
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335 boxOutPng <- makeOut("boxplots.png")
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336 boxOutPdf <- makeOut("boxplots.pdf")
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337 mdsscreeOutPng <- makeOut("mdsscree.png")
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338 mdsscreeOutPdf <- makeOut("mdsscree.pdf")
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339 mdsxOutPdf <- makeOut("mdsplot_extra.pdf")
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340 mdsxOutPng <- makeOut("mdsplot_extra.png")
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341 mdsamOutPdf <- makeOut("mdplots_samples.pdf")
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342 mdOutPdf <- character() # Initialise character vector
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343 volOutPdf <- character()
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344 heatOutPdf <- character()
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345 stripOutPdf <- character()
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346 mdvolOutPng <- character()
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347 topOut <- character()
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348 glimmaOut <- character()
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349 for (i in 1:length(contrastData)) {
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350 con <- contrastData[i]
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351 con <- gsub("\\(|\\)", "", con)
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352 mdOutPdf[i] <- makeOut(paste0("mdplot_", con, ".pdf"))
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353 volOutPdf[i] <- makeOut(paste0("volplot_", con, ".pdf"))
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354 heatOutPdf[i] <- makeOut(paste0("heatmap_", con, ".pdf"))
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355 stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
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356 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
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357 topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
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358 glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
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359 }
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360
3
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361 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
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362 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
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363 sessionOut <- makeOut("session_info.txt")
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364
3
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365 # Initialise data for html links and images, data frame with columns Label and
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366 # Link
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367 linkData <- data.frame(Label=character(), Link=character(),
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368 stringsAsFactors=FALSE)
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369 imageData <- data.frame(Label=character(), Link=character(),
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370 stringsAsFactors=FALSE)
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371
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372 # Initialise vectors for storage of up/down/neutral regulated counts
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373 upCount <- numeric()
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374 downCount <- numeric()
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375 flatCount <- numeric()
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376
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377 ################################################################################
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378 ### Data Processing
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379 ################################################################################
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380
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381 # Extract counts and annotation data
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382 print("Extracting counts")
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383 data <- list()
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384 data$counts <- counts
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385 if (haveAnno) {
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386 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
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387 annoord <- geneanno[match(row.names(counts), geneanno[,1]), ]
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388 data$genes <- annoord
0
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389 } else {
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390 data$genes <- data.frame(GeneID=row.names(counts))
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391 }
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392
8
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393 # Creating naming data
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394 samplenames <- colnames(data$counts)
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395 sampleanno <- data.frame("sampleID"=samplenames, factors)
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396
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397 # Creating colours for the groups
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398 cols <- as.numeric(factors[, 1])
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399 col.group <- palette()[cols]
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400
3
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401 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
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402 # samples. Default is no filtering
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403 preFilterCount <- nrow(data$counts)
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404 nsamples <- ncol(data$counts)
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405
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406 if (filtCPM || filtSmpCount || filtTotCount) {
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407
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408 if (filtTotCount) {
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409 keep <- rowSums(data$counts) >= opt$cntReq
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410 } else if (filtSmpCount) {
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411 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
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412 } else if (filtCPM) {
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413 myCPM <- cpm(data$counts)
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414 thresh <- myCPM >= opt$cpmReq
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415 keep <- rowSums(thresh) >= opt$sampleReq
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416
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417 if ("c" %in% plots) {
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418 # Plot CPM vs raw counts (to check threshold)
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419 pdf(cpmOutPdf, width=6.5, height=10)
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420 par(mfrow=c(3, 2))
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421 for (i in 1:nsamples) {
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422 plot(data$counts[, i], myCPM[, i], xlim=c(0,50), ylim=c(0,3), main=samplenames[i], xlab="Raw counts", ylab="CPM")
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423 abline(v=10, col="red", lty=2, lwd=2)
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424 abline(h=opt$cpmReq, col=4)
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425 }
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426 linkName <- "CpmPlots.pdf"
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427 linkAddr <- "cpmplots.pdf"
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428 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
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429 invisible(dev.off())
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430 }
3
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431 }
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432
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433 data$counts <- data$counts[keep, ]
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434 data$genes <- data$genes[keep, , drop=FALSE]
8
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435
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436 # Plot Density
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437 if ("d" %in% plots) {
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diff changeset
438 # PNG
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439 png(denOutPng, width=1000, height=500)
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diff changeset
440 par(mfrow=c(1,2), cex.axis=0.8)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
441
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
442 # before filtering
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
443 lcpm1 <- cpm(counts, log=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
444 plot(density(lcpm1[, 1]), col=col.group[1], lwd=2, las=2, main="", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
445 title(main="Density Plot: Raw counts", xlab="Log-cpm")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
446 for (i in 2:nsamples){
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
447 den <- density(lcpm1[, i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
448 lines(den$x, den$y, col=col.group[i], lwd=2)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
449 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
450
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
451 # after filtering
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
452 lcpm2 <- cpm(data$counts, log=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
453 plot(density(lcpm2[,1]), col=col.group[1], lwd=2, las=2, main="", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
454 title(main="Density Plot: Filtered counts", xlab="Log-cpm")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
455 for (i in 2:nsamples){
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
456 den <- density(lcpm2[, i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
457 lines(den$x, den$y, col=col.group[i], lwd=2)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
458 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
459 legend("topright", samplenames, text.col=col.group, bty="n")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
460 imgName <- "Densityplots.png"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
461 imgAddr <- "densityplots.png"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
462 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
463 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
464
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
465 # PDF
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
466 pdf(denOutPdf, width=14)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
467 par(mfrow=c(1,2), cex.axis=0.8)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
468 plot(density(lcpm1[, 1]), col=col.group[1], lwd=2, las=2, main="", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
469 title(main="Density Plot: Raw counts", xlab="Log-cpm")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
470 for (i in 2:nsamples){
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
471 den <- density(lcpm1[, i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
472 lines(den$x, den$y, col=col.group[i], lwd=2)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
473 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
474 plot(density(lcpm2[, 1]), col=col.group[1], lwd=2, las=2, main="", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
475 title(main="Density Plot: Filtered counts", xlab="Log-cpm")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
476 for (i in 2:nsamples){
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
477 den <- density(lcpm2[, i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
478 lines(den$x, den$y, col=col.group[i], lwd=2)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
479 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
480 legend("topright", samplenames, text.col=col.group, bty="n")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
481 linkName <- "DensityPlots.pdf"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
482 linkAddr <- "densityplots.pdf"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
483 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
484 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
485 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
486 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
487
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
488 postFilterCount <- nrow(data$counts)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
489 filteredCount <- preFilterCount-postFilterCount
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
490
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
491 # Generating the DGEList object "y"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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492 print("Generating DGEList object")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
493 data$samples <- sampleanno
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
494 data$samples$lib.size <- colSums(data$counts)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
495 data$samples$norm.factors <- 1
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
496 row.names(data$samples) <- colnames(data$counts)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
497 y <- new("DGEList", data)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
498
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
499 print("Generating Design")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
500 # Name rows of factors according to their sample
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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501 row.names(factors) <- names(data$counts)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
502 factorList <- sapply(names(factors), pasteListName)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
503 formula <- "~0"
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
504 for (i in 1:length(factorList)) {
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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diff changeset
505 formula <- paste(formula,factorList[i], sep="+")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
506 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
507 formula <- formula(formula)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
508 design <- model.matrix(formula)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
509 for (i in 1:length(factorList)) {
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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diff changeset
510 colnames(design) <- gsub(factorList[i], "", colnames(design), fixed=TRUE)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
511 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
512
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
513 # Calculating normalising factors
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
514 print("Calculating Normalisation Factors")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
515 y <- calcNormFactors(y, method=opt$normOpt)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
516
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
diff changeset
517 # Generate contrasts information
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
518 print("Generating Contrasts")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
519 contrasts <- makeContrasts(contrasts=contrastData, levels=design)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
520
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
521 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
522 ### Data Output
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
523 ################################################################################
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
524
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
525 # Plot Box plots (before and after normalisation)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
526 if (opt$normOpt != "none" & "b" %in% plots) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
527 png(boxOutPng, width=1000, height=500)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
528 par(mfrow=c(1,2), mar=c(6,4,2,2)+0.1)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
529 labels <- colnames(counts)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
530
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
531 lcpm1 <- cpm(y$counts, log=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
532 boxplot(lcpm1, las=2, col=col.group, xaxt="n", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
533 axis(1, at=seq_along(labels), labels = FALSE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
534 abline(h=median(lcpm1), col=4)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
535 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
536 title(main="Box Plot: Unnormalised counts", ylab="Log-cpm")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
537
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
538 lcpm2 <- cpm(y, log=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
539 boxplot(lcpm2, las=2, col=col.group, xaxt="n", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
540 axis(1, at=seq_along(labels), labels = FALSE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
541 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
542 abline(h=median(lcpm2), col=4)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
543 title(main="Box Plot: Normalised counts", ylab="Log-cpm")
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
544
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
545 imgName <- "Boxplots.png"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
546 imgAddr <- "boxplots.png"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
547 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
548 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
549
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
550 pdf(boxOutPdf, width=14)
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
551 par(mfrow=c(1,2), mar=c(6,4,2,2)+0.1)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
552 boxplot(lcpm1, las=2, col=col.group, xaxt="n", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
553 axis(1, at=seq_along(labels), labels = FALSE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
554 abline(h=median(lcpm1), col=4)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
555 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
556 title(main="Box Plot: Unnormalised counts", ylab="Log-cpm")
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
557 boxplot(lcpm2, las=2, col=col.group, xaxt="n", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
558 axis(1, at=seq_along(labels), labels = FALSE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
559 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
560 abline(h=median(lcpm2), col=4)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
561 title(main="Box Plot: Normalised counts", ylab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
562 linkName <- "BoxPlots.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
563 linkAddr <- "boxplots.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
564 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
565 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
566 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
567
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
568 # Plot MDS
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
569 print("Generating MDS plot")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
570 labels <- names(counts)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
571
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
572 # Scree plot (Variance Explained) code copied from Glimma
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
573
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
574 # get column of matrix
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
575 getCols <- function(x, inds) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
576 x[, inds, drop=FALSE]
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
577 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
578
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
579 x <- cpm(y, log=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
580 ndim <- nsamples - 1
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
581 nprobes <- nrow(x)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
582 top <- 500
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
583 top <- min(top, nprobes)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
584 cn <- colnames(x)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
585 bad <- rowSums(is.finite(x)) < nsamples
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
586
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
587 if (any(bad)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
588 warning("Rows containing infinite values have been removed")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
589 x <- x[!bad, , drop=FALSE]
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
590 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
591
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
592 dd <- matrix(0, nrow=nsamples, ncol=nsamples, dimnames=list(cn, cn))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
593 topindex <- nprobes - top + 1L
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
594 for (i in 2L:(nsamples)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
595 for (j in 1L:(i - 1L)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
596 dists <- (getCols(x, i) - getCols(x, j))^2
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
597 dists <- sort.int(dists, partial = topindex )
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
598 topdist <- dists[topindex:nprobes]
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
599 dd[i, j] <- sqrt(mean(topdist))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
600 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
601 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
602
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
603 a1 <- suppressWarnings(cmdscale(as.dist(dd), k=min(ndim, 8), eig=TRUE))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
604 eigen <- data.frame(name = 1:min(ndim, 8), eigen = round(a1$eig[1:min(ndim, 8)]/sum(a1$eig), 2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
605
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
606 png(mdsscreeOutPng, width=1000, height=500)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
607 par(mfrow=c(1, 2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
608 plotMDS(y, labels=samplenames, col=as.numeric(factors[, 1]), main="MDS Plot: Dims 1 and 2")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
609 barplot(eigen$eigen, names.arg=eigen$name, main = "Scree Plot: Variance Explained", xlab = "Dimension", ylab = "Proportion", las=1)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
610 imgName <- paste0("MDSPlot_", names(factors)[1], ".png")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
611 imgAddr <- "mdsscree.png"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
612 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
613 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
614
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
615 pdf(mdsscreeOutPdf, width=14)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
616 par(mfrow=c(1, 2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
617 plotMDS(y, labels=samplenames, col=as.numeric(factors[, 1]), main="MDS Plot: Dims 1 and 2")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
618 barplot(eigen$eigen, names.arg=eigen$name, main = "Scree Plot: Variance Explained", xlab = "Dimension", ylab = "Proportion", las=1)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
619 linkName <- paste0("MDSPlot_", names(factors)[1], ".pdf")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
620 linkAddr <- "mdsscree.pdf"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
621 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
622 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
623
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
624 if ("x" %in% plots) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
625 png(mdsxOutPng, width=1000, height=500)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
626 par(mfrow=c(1, 2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
627 for (i in 2:3) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
628 dim1 <- i
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
629 dim2 <- i + 1
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
630 plotMDS(y, dim=c(dim1, dim2), labels=samplenames, col=as.numeric(factors[, 1]), main=paste("MDS Plot: Dims", dim1, "and", dim2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
631 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
632 imgName <- paste0("MDSPlot_extra.png")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
633 imgAddr <- paste0("mdsplot_extra.png")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
634 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
635 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
636
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
637 pdf(mdsxOutPdf, width=14)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
638 par(mfrow=c(1, 2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
639 for (i in 2:3) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
640 dim1 <- i
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
641 dim2 <- i + 1
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
642 plotMDS(y, dim=c(dim1, dim2), labels=samplenames, col=as.numeric(factors[, 1]), main=paste("MDS Plot: Dims", dim1, "and", dim2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
643 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
644 linkName <- "MDSPlot_extra.pdf"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
645 linkAddr <- "mdsplot_extra.pdf"
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
646 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
647 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
648 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
649
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
650 if ("m" %in% plots) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
651 # Plot MD plots for individual samples
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
652 print("Generating MD plots for samples")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
653 pdf(mdsamOutPdf, width=6.5, height=10)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
654 par(mfrow=c(3, 2))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
655 for (i in 1:nsamples) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
656 plotMD(y, column = i)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
657 abline(h=0, col="red", lty=2, lwd=2)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
658 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
659 linkName <- "MDPlots_Samples.pdf"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
660 linkAddr <- "mdplots_samples.pdf"
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
661 linkData <- rbind(linkData, c(linkName, linkAddr))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
662 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
663 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
664
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
665
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
666 if (wantTrend) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
667 # limma-trend approach
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
668 logCPM <- cpm(y, log=TRUE, prior.count=opt$trend)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
669 fit <- lmFit(logCPM, design)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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parents: 5
diff changeset
670 fit$genes <- y$genes
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
671 fit <- contrasts.fit(fit, contrasts)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
672 if (wantRobust) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
673 fit <- eBayes(fit, trend=TRUE, robust=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
674 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
675 fit <- eBayes(fit, trend=TRUE, robust=FALSE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
676 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
677 # plot fit with plotSA
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
678 saOutPng <- makeOut("saplot.png")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
679 saOutPdf <- makeOut("saplot.pdf")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
680
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
681 png(saOutPng, width=500, height=500)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
682 plotSA(fit, main="SA Plot")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
683 imgName <- "SAPlot.png"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
684 imgAddr <- "saplot.png"
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
685 imageData <- rbind(imageData, c(imgName, imgAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
686 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
687
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
688 pdf(saOutPdf, width=14)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
689 plotSA(fit, main="SA Plot")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
690 linkName <- "SAPlot.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
691 linkAddr <- "saplot.pdf"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
692 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
693 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
694
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
695 plotData <- logCPM
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
696
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
697 # Save normalised counts (log2cpm)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
698 if (wantNorm) {
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
699 write.table(logCPM, file=normOut, row.names=TRUE, sep="\t", quote=FALSE)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
700 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv"))))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
701 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
702 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
703 # limma-voom approach
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
704 voomOutPdf <- makeOut("voomplot.pdf")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
705 voomOutPng <- makeOut("voomplot.png")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
706
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
707 if (wantWeight) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
708 # Creating voom data object and plot
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
709 png(voomOutPng, width=1000, height=500)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
710 vData <- voomWithQualityWeights(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
711 imgName <- "VoomPlot.png"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
712 imgAddr <- "voomplot.png"
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
713 imageData <- rbind(imageData, c(imgName, imgAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
714 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
715
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
716 pdf(voomOutPdf, width=14)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
717 vData <- voomWithQualityWeights(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
718 linkName <- "VoomPlot.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
719 linkAddr <- "voomplot.pdf"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
720 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
721 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
722
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
723 # Generating fit data and top table with weights
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
724 wts <- vData$weights
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
725 voomFit <- lmFit(vData, design, weights=wts)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
726
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
727 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
728 # Creating voom data object and plot
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
729 png(voomOutPng, width=500, height=500)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
730 vData <- voom(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
731 imgName <- "VoomPlot"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
732 imgAddr <- "voomplot.png"
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
733 imageData <- rbind(imageData, c(imgName, imgAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
734 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
735
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
736 pdf(voomOutPdf)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
737 vData <- voom(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
738 linkName <- "VoomPlot.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
739 linkAddr <- "voomplot.pdf"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
740 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
741 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
742
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
743 # Generate voom fit
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
744 voomFit <- lmFit(vData, design)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
745 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
746
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
747 # Save normalised counts (log2cpm)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
748 if (wantNorm) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
749 norm_counts <- data.frame(vData$genes, vData$E)
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
750 write.table(norm_counts, file=normOut, row.names=FALSE, sep="\t", quote=FALSE)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
751 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv"))))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
752 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
753
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
754 # Fit linear model and estimate dispersion with eBayes
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
755 voomFit <- contrasts.fit(voomFit, contrasts)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
756 if (wantRobust) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
757 fit <- eBayes(voomFit, robust=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
758 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
759 fit <- eBayes(voomFit, robust=FALSE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
760 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
761 plotData <- vData
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
762 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
763
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
764
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
765 print("Generating DE results")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
766
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
767 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
768 print("Applying TREAT method")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
769 if (wantRobust) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
770 fit <- treat(fit, lfc=opt$lfcReq, robust=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
771 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
772 fit <- treat(fit, lfc=opt$lfcReq, robust=FALSE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
773 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
774 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
775
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
776 status = decideTests(fit, adjust.method=opt$pAdjOpt, p.value=opt$pValReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
777 lfc=opt$lfcReq)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
778 sumStatus <- summary(status)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
779
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
780 for (i in 1:length(contrastData)) {
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
781 con <- contrastData[i]
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
782 con <- gsub("\\(|\\)", "", con)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
783 # Collect counts for differential expression
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
784 upCount[i] <- sumStatus["Up", i]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
785 downCount[i] <- sumStatus["Down", i]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
786 flatCount[i] <- sumStatus["NotSig", i]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
787
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
788 # Write top expressions table
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
789 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
790 top <- topTreat(fit, coef=i, number=Inf, sort.by="P")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
791 } else{
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
792 top <- topTable(fit, coef=i, number=Inf, sort.by="P")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
793 }
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
794 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE)
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
795 linkName <- paste0(deMethod, "_", con, ".tsv")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
796 linkAddr <- paste0(deMethod, "_", con, ".tsv")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
797 linkData <- rbind(linkData, c(linkName, linkAddr))
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
798
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
799 # Plot MD (log ratios vs mean average) using limma package on weighted
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
800 pdf(mdOutPdf[i])
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
801 limma::plotMD(fit, status=status[, i], coef=i,
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
802 main=paste("MD Plot:", unmake.names(con)),
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
803 hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1),
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
804 xlab="Average Expression", ylab="logFC")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
805 abline(h=0, col="grey", lty=2)
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
806 linkName <- paste0("MDPlot_", con, ".pdf")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
807 linkAddr <- paste0("mdplot_", con, ".pdf")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
808 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
809 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
810
10
e26047c4562d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents: 9
diff changeset
811 # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene labels/symbols in 2nd column)
9
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
812 if (haveAnno) {
10
e26047c4562d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents: 9
diff changeset
813 # make gene labels unique to handle NAs
e26047c4562d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents: 9
diff changeset
814 geneanno <- y$genes
e26047c4562d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents: 9
diff changeset
815 geneanno[, 2] <- make.unique(geneanno[, 2])
e26047c4562d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents: 9
diff changeset
816 Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1],
9
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
817 status=status[, i], sample.cols=col.group,
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
818 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2],
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
819 folder=paste0("glimma_", unmake.names(con)), launch=FALSE)
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
820 linkName <- paste0("Glimma_MDPlot_", con, ".html")
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
821 linkAddr <- paste0("glimma_", con, "/MD-Plot.html")
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
822 linkData <- rbind(linkData, c(linkName, linkAddr))
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
823 }
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
824
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
825 # Plot Volcano
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
826 pdf(volOutPdf[i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
827 if (haveAnno) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
828 # labels must be in second column currently
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
829 labels <- fit$genes[, 2]
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
830 } else {
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
831 labels <- fit$genes$GeneID
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
832 }
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
833 limma::volcanoplot(fit, coef=i,
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
834 main=paste("Volcano Plot:", unmake.names(con)),
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
835 highlight=opt$topgenes,
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
836 names=labels)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
837 linkName <- paste0("VolcanoPlot_", con, ".pdf")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
838 linkAddr <- paste0("volplot_", con, ".pdf")
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
839 linkData <- rbind(linkData, c(linkName, linkAddr))
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
840 invisible(dev.off())
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
841
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
842 # PNG of MD and Volcano
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
843 png(mdvolOutPng[i], width=1000, height=500)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
844 par(mfrow=c(1, 2), mar=c(5,4,2,2)+0.1, oma=c(0,0,3,0))
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
845
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
846 # MD plot
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
847 limma::plotMD(fit, status=status[, i], coef=i, main="MD Plot",
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
848 hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1),
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
849 xlab="Average Expression", ylab="logFC")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
850 abline(h=0, col="grey", lty=2)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
851
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
852 # Volcano
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
853 if (haveAnno) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
854 # labels must be in second column currently
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
855 limma::volcanoplot(fit, coef=i, main="Volcano Plot",
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
856 highlight=opt$topgenes,
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
857 names=fit$genes[, 2])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
858 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
859 limma::volcanoplot(fit, coef=i, main="Volcano Plot",
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
860 highlight=opt$topgenes,
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
861 names=fit$genes$GeneID)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
862 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
863
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
864 imgName <- paste0("MDVolPlot_", con)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
865 imgAddr <- paste0("mdvolplot_", con, ".png")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
866 imageData <- rbind(imageData, c(imgName, imgAddr))
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
867 title(paste0("Contrast: ", unmake.names(con)), outer=TRUE, cex.main=1.5)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
868 invisible(dev.off())
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
869
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
870 if ("h" %in% plots) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
871 # Plot Heatmap
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
872 topgenes <- rownames(top[1:opt$topgenes, ])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
873 if (wantTrend) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
874 topexp <- plotData[topgenes, ]
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
875 } else {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
876 topexp <- plotData$E[topgenes, ]
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
877 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
878 pdf(heatOutPdf[i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
879 mycol <- colorpanel(1000,"blue","white","red")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
880 if (haveAnno) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
881 # labels must be in second column currently
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
882 labels <- top[topgenes, 2]
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
883 } else {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
884 labels <- rownames(topexp)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
885 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
886 heatmap.2(topexp, scale="row", Colv=FALSE, Rowv=FALSE, dendrogram="none",
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
887 main=paste("Contrast:", unmake.names(con), "\nTop", opt$topgenes, "genes by adj.P.Val"),
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
888 trace="none", density.info="none", lhei=c(2,10), margin=c(8, 6), labRow=labels, cexRow=0.7, srtCol=45,
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
889 col=mycol, ColSideColors=col.group)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
890 linkName <- paste0("Heatmap_", con, ".pdf")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
891 linkAddr <- paste0("heatmap_", con, ".pdf")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
892 linkData <- rbind(linkData, c(linkName, linkAddr))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
893 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
894 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
895
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
896 if ("s" %in% plots) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
897 # Plot Stripcharts of top genes
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
898 pdf(stripOutPdf[i], title=paste("Contrast:", unmake.names(con)))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
899 par(mfrow = c(3,2), cex.main=0.8, cex.axis=0.8)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
900 cols <- unique(col.group)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
901
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
902 for (j in 1:length(topgenes)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
903 lfc <- round(top[topgenes[j], "logFC"], 2)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
904 pval <- round(top[topgenes[j], "adj.P.Val"], 5)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
905 if (wantTrend) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
906 stripchart(plotData[topgenes[j], ] ~ factors[, 1], vertical=TRUE, las=2, pch=16, cex=0.8, cex.lab=0.8, col=cols,
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
907 method="jitter", ylab="Normalised log2 expression", main=paste0(labels[j], "\nlogFC=", lfc, ", adj.P.Val=", pval))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
908 } else {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
909 stripchart(plotData$E[topgenes[j], ] ~ factors[, 1], vertical=TRUE, las=2, pch=16, cex=0.8, cex.lab=0.8, col=cols,
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
910 method="jitter", ylab="Normalised log2 expression", main=paste0(labels[j], "\nlogFC=", lfc, ", adj.P.Val=", pval))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
911 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
912 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
913 linkName <- paste0("Stripcharts_", con, ".pdf")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
914 linkAddr <- paste0("stripcharts_", con, ".pdf")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
915 linkData <- rbind(linkData, c(linkName, linkAddr))
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
916 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
917 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
918 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
919 sigDiff <- data.frame(Up=upCount, Flat=flatCount, Down=downCount)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
920 row.names(sigDiff) <- contrastData
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
921
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
922 # Save relevant items as rda object
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
923 if (wantRda) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
924 print("Saving RData")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
925 if (wantWeight) {
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
926 save(counts, data, y, status, plotData, labels, factors, wts, fit, top, contrastData, contrasts, design,
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
927 file=rdaOut, ascii=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
928 } else {
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
929 save(counts, data, y, status, plotData, labels, factors, fit, top, contrastData, contrasts, design,
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
930 file=rdaOut, ascii=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
931 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
932 linkData <- rbind(linkData, c((paste0(deMethod, "_analysis.RData")), (paste0(deMethod, "_analysis.RData"))))
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
933 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
934
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
935 # Record session info
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
936 writeLines(capture.output(sessionInfo()), sessionOut)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
937 linkData <- rbind(linkData, c("Session Info", "session_info.txt"))
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
938
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
939 # Record ending time and calculate total run time
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
940 timeEnd <- as.character(Sys.time())
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
941 timeTaken <- capture.output(round(difftime(timeEnd,timeStart), digits=3))
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
942 timeTaken <- gsub("Time difference of ", "", timeTaken, fixed=TRUE)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
943 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
944 ### HTML Generation
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
945 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
946
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
947 # Clear file
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
948 cat("", file=opt$htmlPath)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
949
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
950 cata("<html>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
951
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
952 cata("<body>\n")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
953 cata("<h3>Limma Analysis Output:</h3>\n")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
954 cata("Links to PDF copies of plots are in 'Plots' section below <br />\n")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
955
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
956 for (i in 1:nrow(imageData)) {
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
957 if (grepl("density|box|mds|mdvol", imageData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
958 HtmlImage(imageData$Link[i], imageData$Label[i], width=1000)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
959 } else if (wantWeight) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
960 HtmlImage(imageData$Link[i], imageData$Label[i], width=1000)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
961 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
962 HtmlImage(imageData$Link[i], imageData$Label[i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
963 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
964 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
965
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
966 cata("<h4>Differential Expression Counts:</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
967
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
968 cata("<table border=\"1\" cellpadding=\"4\">\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
969 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
970 TableItem()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
971 for (i in colnames(sigDiff)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
972 TableHeadItem(i)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
973 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
974 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
975 for (i in 1:nrow(sigDiff)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
976 cata("<tr>\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
977 TableHeadItem(unmake.names(row.names(sigDiff)[i]))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
978 for (j in 1:ncol(sigDiff)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
979 TableItem(as.character(sigDiff[i, j]))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
980 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
981 cata("</tr>\n")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
982 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
983 cata("</table>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
984
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
985 cata("<h4>Plots:</h4>\n")
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
986 #PDFs
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
987 for (i in 1:nrow(linkData)) {
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
988 if (grepl("density|cpm|boxplot|mds|mdplots|voomplot|saplot", linkData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
989 HtmlLink(linkData$Link[i], linkData$Label[i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
990 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
991 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
992
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
993 for (i in 1:nrow(linkData)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
994 if (grepl("mdplot_", linkData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
995 HtmlLink(linkData$Link[i], linkData$Label[i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
996 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
997 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
998
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
999 for (i in 1:nrow(linkData)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1000 if (grepl("volplot", linkData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1001 HtmlLink(linkData$Link[i], linkData$Label[i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1002 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1003 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1004
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1005 for (i in 1:nrow(linkData)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1006 if (grepl("heatmap", linkData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1007 HtmlLink(linkData$Link[i], linkData$Label[i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1008 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1009 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1010
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1011 for (i in 1:nrow(linkData)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1012 if (grepl("stripcharts", linkData$Link[i])) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1013 HtmlLink(linkData$Link[i], linkData$Label[i])
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1014 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1015 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1016
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1017 cata("<h4>Tables:</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1018 for (i in 1:nrow(linkData)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1019 if (grepl(".tsv", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1020 HtmlLink(linkData$Link[i], linkData$Label[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1021 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1022 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1023
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1024 if (wantRda) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1025 cata("<h4>R Data Object:</h4>\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1026 for (i in 1:nrow(linkData)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1027 if (grepl(".RData", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1028 HtmlLink(linkData$Link[i], linkData$Label[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1029 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1030 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1031 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1032
9
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1033 cata("<h4>Glimma Interactive Results:</h4>\n")
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1034 for (i in 1:nrow(linkData)) {
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1035 if (grepl("glimma", linkData$Link[i])) {
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1036 HtmlLink(linkData$Link[i], linkData$Label[i])
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1037 }
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1038 }
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1039
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1040 cata("<p>Alt-click links to download file.</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1041 cata("<p>Click floppy disc icon associated history item to download ")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1042 cata("all files.</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1043 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1044
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1045 cata("<h4>Additional Information</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1046 cata("<ul>\n")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1047
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1048 if (filtCPM || filtSmpCount || filtTotCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1049 if (filtCPM) {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
1050 tempStr <- paste("Genes without more than", opt$cpmReq,
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1051 "CPM in at least", opt$sampleReq, "samples are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1052 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1053 } else if (filtSmpCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1054 tempStr <- paste("Genes without more than", opt$cntReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1055 "counts in at least", opt$sampleReq, "samples are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1056 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1057 } else if (filtTotCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1058 tempStr <- paste("Genes without more than", opt$cntReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1059 "counts, after summing counts for all samples, are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1060 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1061 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1062
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1063 ListItem(tempStr)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1064 filterProp <- round(filteredCount/preFilterCount*100, digits=2)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1065 tempStr <- paste0(filteredCount, " of ", preFilterCount," (", filterProp,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1066 "%) genes were filtered out for low expression.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1067 ListItem(tempStr)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1068 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1069 ListItem(opt$normOpt, " was the method used to normalise library sizes.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1070 if (wantTrend) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1071 ListItem("The limma-trend method was used.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1072 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1073 ListItem("The limma-voom method was used.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1074 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1075 if (wantWeight) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1076 ListItem("Weights were applied to samples.")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1077 } else {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1078 ListItem("Weights were not applied to samples.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1079 }
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1080 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1081 ListItem(paste("Testing significance relative to a fold-change threshold (TREAT) was performed using a threshold of log2 =", opt$lfcReq, "at FDR of", opt$pValReq, "."))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1082 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1083 if (wantRobust) {
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1084 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1085 ListItem("TREAT was used with robust settings (robust=TRUE).")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1086 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1087 ListItem("eBayes was used with robust settings (robust=TRUE).")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1088 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1089 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1090 if (opt$pAdjOpt!="none") {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1091 if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
1092 tempStr <- paste0("MD Plot highlighted genes are significant at FDR ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1093 "of ", opt$pValReq," and exhibit log2-fold-change of at ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1094 "least ", opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1095 ListItem(tempStr)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1096 } else if (opt$pAdjOpt=="holm") {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
1097 tempStr <- paste0("MD Plot highlighted genes are significant at adjusted ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1098 "p-value of ", opt$pValReq," by the Holm(1979) ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1099 "method, and exhibit log2-fold-change of at least ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1100 opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1101 ListItem(tempStr)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1102 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1103 } else {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
1104 tempStr <- paste0("MD Plot highlighted genes are significant at p-value ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1105 "of ", opt$pValReq," and exhibit log2-fold-change of at ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1106 "least ", opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1107 ListItem(tempStr)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1108 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1109 cata("</ul>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1110
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1111 cata("<h4>Summary of experimental data:</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1112
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
1113 cata("<p>*CHECK THAT SAMPLES ARE ASSOCIATED WITH CORRECT GROUP(S)*</p>\n")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1114
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1115 cata("<table border=\"1\" cellpadding=\"3\">\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1116 cata("<tr>\n")
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
1117 TableHeadItem("SampleID")
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
1118 TableHeadItem(names(factors)[1]," (Primary Factor)")
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
1119
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1120 if (ncol(factors) > 1) {
2
a330ddf43861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents: 1
diff changeset
1121 for (i in names(factors)[2:length(names(factors))]) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1122 TableHeadItem(i)
2
a330ddf43861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents: 1
diff changeset
1123 }
a330ddf43861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents: 1
diff changeset
1124 cata("</tr>\n")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1125 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1126
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1127 for (i in 1:nrow(factors)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1128 cata("<tr>\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1129 TableHeadItem(row.names(factors)[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1130 for (j in 1:ncol(factors)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1131 TableItem(as.character(unmake.names(factors[i, j])))
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1132 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1133 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1134 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1135 cata("</table>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1136
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1137 cit <- character()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1138 link <- character()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1139 link[1] <- paste0("<a href=\"",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1140 "http://www.bioconductor.org/packages/release/bioc/",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1141 "vignettes/limma/inst/doc/usersguide.pdf",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1142 "\">", "limma User's Guide", "</a>.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1143
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1144 link[2] <- paste0("<a href=\"",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1145 "http://www.bioconductor.org/packages/release/bioc/",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1146 "vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1147 "\">", "edgeR User's Guide", "</a>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1148
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1149 cit[1] <- paste("Please cite the following paper for this tool:")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1150
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1151 cit[2] <- paste("Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME,",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1152 "Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? ",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1153 "Modelling sample and observational level variability improves power ",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1154 "in RNA-seq analyses. Nucleic Acids Research, 43(15), e97.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1155
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1156 cit[3] <- paste("Please cite the paper below for the limma software itself.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1157 "Please also try to cite the appropriate methodology articles",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1158 "that describe the statistical methods implemented in limma,",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1159 "depending on which limma functions you are using. The",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1160 "methodology articles are listed in Section 2.1 of the",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1161 link[1],
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1162 "Cite no. 3 only if sample weights were used.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1163 cit[4] <- paste("Smyth GK (2005). Limma: linear models for microarray data.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1164 "In: 'Bioinformatics and Computational Biology Solutions using",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1165 "R and Bioconductor'. R. Gentleman, V. Carey, S. doit,.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1166 "Irizarry, W. Huber (eds), Springer, New York, pages 397-420.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1167 cit[5] <- paste("Please cite the first paper for the software itself and the",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1168 "other papers for the various original statistical methods",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1169 "implemented in edgeR. See Section 1.2 in the", link[2],
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1170 "for more detail.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1171 cit[6] <- paste("Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1172 "Bioconductor package for differential expression analysis",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1173 "of digital gene expression data. Bioinformatics 26, 139-140")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1174 cit[7] <- paste("Robinson MD and Smyth GK (2007). Moderated statistical tests",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1175 "for assessing differences in tag abundance. Bioinformatics",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1176 "23, 2881-2887")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1177 cit[8] <- paste("Robinson MD and Smyth GK (2008). Small-sample estimation of",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1178 "negative binomial dispersion, with applications to SAGE data.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1179 "Biostatistics, 9, 321-332")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1180 cit[9] <- paste("McCarthy DJ, Chen Y and Smyth GK (2012). Differential",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1181 "expression analysis of multifactor RNA-Seq experiments with",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1182 "respect to biological variation. Nucleic Acids Research 40,",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1183 "4288-4297")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1184 cit[10] <- paste("Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1185 "precision weights unlock linear model analysis tools for",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1186 "RNA-seq read counts. Genome Biology 15, R29.")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1187 cit[11] <- paste("Ritchie ME, Diyagama D, Neilson J, van Laar R,",
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1188 "Dobrovic A, Holloway A and Smyth GK (2006).",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1189 "Empirical array quality weights for microarray data.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1190 "BMC Bioinformatics 7, Article 261.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1191 cata("<h3>Citations</h3>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1192 cata(cit[1], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1193 cata("<br>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1194 cata(cit[2], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1195
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1196 cata("<h4>limma</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1197 cata(cit[3], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1198 cata("<ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1199 ListItem(cit[4])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1200 ListItem(cit[10])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1201 ListItem(cit[11])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1202 cata("</ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1203
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1204 cata("<h4>edgeR</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1205 cata(cit[5], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1206 cata("<ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1207 ListItem(cit[6])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1208 ListItem(cit[7])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1209 ListItem(cit[8])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1210 ListItem(cit[9])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1211 cata("</ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1212
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1213 cata("<p>Please report problems or suggestions to: su.s@wehi.edu.au</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1214
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1215 for (i in 1:nrow(linkData)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1216 if (grepl("session_info", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1217 HtmlLink(linkData$Link[i], linkData$Label[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1218 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1219 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1220
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1221 cata("<table border=\"0\">\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1222 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1223 TableItem("Task started at:"); TableItem(timeStart)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1224 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1225 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1226 TableItem("Task ended at:"); TableItem(timeEnd)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1227 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1228 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1229 TableItem("Task run time:"); TableItem(timeTaken)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1230 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1231 cata("</table>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1232
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1233 cata("</body>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1234 cata("</html>")