Mercurial > repos > iuc > limma_voom

annotate limma_voom.R @ 12:81796eb60bd0 draft

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author iuc
date Sun, 05 Aug 2018 05:13:12 -0400
parents 7e8af58c8052
children d5a940112511
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1 # This tool takes in a matrix of feature counts as well as gene annotations and
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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 "filtCounts", "F", 0, "logical",
3
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170 "normCounts", "x", 0, "logical",
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171 "rdaOpt", "r", 0, "logical",
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172 "lfcReq", "l", 1, "double",
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173 "pValReq", "p", 1, "double",
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iuc
parents: 2
diff changeset
174 "pAdjOpt", "d", 1, "character",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
175 "normOpt", "n", 1, "character",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
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176 "robOpt", "b", 0, "logical",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
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177 "trend", "t", 1, "double",
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
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178 "weightOpt", "w", 0, "logical",
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
179 "topgenes", "G", 1, "integer",
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
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180 "treatOpt", "T", 0, "logical",
11
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iuc
parents: 10
diff changeset
181 "plots", "P", 1, "character",
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
182 "libinfoOpt", "L", 0, "logical"),
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
183 byrow=TRUE, ncol=4)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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184 opt <- getopt(spec)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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185
1
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iuc
parents: 0
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186
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
187 if (is.null(opt$matrixPath) & is.null(opt$filesPath)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
188 cat("A counts matrix (or a set of counts files) is required.\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
189 q(status=1)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
190 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
191
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
192 if (is.null(opt$cpmReq)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
193 filtCPM <- FALSE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
194 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
195 filtCPM <- TRUE
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
196 }
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
197
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
198 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
199 filtSmpCount <- FALSE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
200 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
201 filtSmpCount <- TRUE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
202 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
203
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
204 if (is.null(opt$totReq)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
205 filtTotCount <- FALSE
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
206 } else {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
207 filtTotCount <- TRUE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
208 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
209
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
210 if (is.null(opt$rdaOpt)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
211 wantRda <- FALSE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
212 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
213 wantRda <- TRUE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
214 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
215
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
216 if (is.null(opt$annoPath)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
217 haveAnno <- FALSE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
218 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
219 haveAnno <- TRUE
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
220 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
221
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
222 if (is.null(opt$filtCounts)) {
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
223 wantFilt <- FALSE
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
224 } else {
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
225 wantFilt <- TRUE
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
226 }
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
227
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
228 if (is.null(opt$normCounts)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
229 wantNorm <- FALSE
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
230 } else {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
231 wantNorm <- TRUE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
232 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
233
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
234 if (is.null(opt$robOpt)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
235 wantRobust <- FALSE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
236 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
237 wantRobust <- TRUE
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
238 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
239
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
240 if (is.null(opt$weightOpt)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
241 wantWeight <- FALSE
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
242 } else {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
243 wantWeight <- TRUE
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
244 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
245
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
246 if (is.null(opt$trend)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
247 wantTrend <- FALSE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
248 deMethod <- "limma-voom"
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
249 } 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
250 wantTrend <- TRUE
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
251 deMethod <- "limma-trend"
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
252 priorCount <- opt$trend
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
253 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
254
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
255 if (is.null(opt$treatOpt)) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
256 wantTreat <- FALSE
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
257 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
258 wantTreat <- TRUE
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
259 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
260
11
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
261 if (is.null(opt$libinfoOpt)) {
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
262 wantLibinfo <- FALSE
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
263 } else {
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
264 wantLibinfo <- TRUE
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
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265 }
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266
0
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267
3
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268 if (!is.null(opt$filesPath)) {
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269 # Process the separate count files (adapted from DESeq2 wrapper)
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270 library("rjson")
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271 parser <- newJSONParser()
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272 parser$addData(opt$filesPath)
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273 factorList <- parser$getObject()
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274 factors <- sapply(factorList, function(x) x[[1]])
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275 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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276 sampleTable <- data.frame(sample=basename(filenamesIn),
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277 filename=filenamesIn,
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278 row.names=filenamesIn,
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279 stringsAsFactors=FALSE)
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280 for (factor in factorList) {
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281 factorName <- factor[[1]]
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282 sampleTable[[factorName]] <- character(nrow(sampleTable))
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283 lvls <- sapply(factor[[2]], function(x) names(x))
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284 for (i in seq_along(factor[[2]])) {
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285 files <- factor[[2]][[i]][[1]]
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286 sampleTable[files,factorName] <- lvls[i]
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287 }
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288 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls)
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289 }
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290 rownames(sampleTable) <- sampleTable$sample
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291 rem <- c("sample","filename")
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292 factors <- sampleTable[, !(names(sampleTable) %in% rem), drop=FALSE]
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293
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294 #read in count files and create single table
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295 countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)})
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296 counts <- do.call("cbind", countfiles)
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297
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298 } else {
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299 # Process the single count matrix
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300 counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", strip.white=TRUE, stringsAsFactors=FALSE)
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301 row.names(counts) <- counts[, 1]
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302 counts <- counts[ , -1]
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303 countsRows <- nrow(counts)
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304
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305 # Process factors
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306 if (is.null(opt$factInput)) {
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307 factorData <- read.table(opt$factFile, header=TRUE, sep="\t", strip.white=TRUE)
3
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308 factors <- factorData[, -1, drop=FALSE]
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309 } else {
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310 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))
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311 factorData <- list()
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312 for (fact in factors) {
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313 newFact <- unlist(strsplit(fact, split="::"))
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314 factorData <- rbind(factorData, newFact)
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315 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
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316
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317 # Set the row names to be the name of the factor and delete first row
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318 row.names(factorData) <- factorData[, 1]
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319 factorData <- factorData[, -1]
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320 factorData <- sapply(factorData, sanitiseGroups)
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321 factorData <- sapply(factorData, strsplit, split=",")
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322 factorData <- sapply(factorData, make.names)
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323 # Transform factor data into data frame of R factor objects
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324 factors <- data.frame(factorData)
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325 }
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326 }
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327
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328 # if annotation file provided
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329 if (haveAnno) {
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330 geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE)
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331 }
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332
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333 #Create output directory
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334 dir.create(opt$outPath, showWarnings=FALSE)
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335
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336 # Split up contrasts seperated by comma into a vector then sanitise
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337 contrastData <- unlist(strsplit(opt$contrastData, split=","))
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338 contrastData <- sanitiseEquation(contrastData)
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339 contrastData <- gsub(" ", ".", contrastData, fixed=TRUE)
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340
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341 plots <- character()
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342 if (!is.null(opt$plots)) {
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343 plots <- unlist(strsplit(opt$plots, split=","))
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344 }
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345
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346 denOutPng <- makeOut("densityplots.png")
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347 denOutPdf <- makeOut("densityplots.pdf")
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348 cpmOutPdf <- makeOut("cpmplots.pdf")
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349 boxOutPng <- makeOut("boxplots.png")
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350 boxOutPdf <- makeOut("boxplots.pdf")
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351 mdsscreeOutPng <- makeOut("mdsscree.png")
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352 mdsscreeOutPdf <- makeOut("mdsscree.pdf")
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353 mdsxOutPdf <- makeOut("mdsplot_extra.pdf")
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354 mdsxOutPng <- makeOut("mdsplot_extra.png")
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355 mdsamOutPdf <- makeOut("mdplots_samples.pdf")
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356 mdOutPdf <- character() # Initialise character vector
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357 volOutPdf <- character()
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358 heatOutPdf <- character()
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359 stripOutPdf <- character()
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360 mdvolOutPng <- character()
0
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361 topOut <- character()
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362 glimmaOut <- character()
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363 for (i in 1:length(contrastData)) {
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364 con <- contrastData[i]
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365 con <- gsub("\\(|\\)", "", con)
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366 mdOutPdf[i] <- makeOut(paste0("mdplot_", con, ".pdf"))
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367 volOutPdf[i] <- makeOut(paste0("volplot_", con, ".pdf"))
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368 heatOutPdf[i] <- makeOut(paste0("heatmap_", con, ".pdf"))
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369 stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf"))
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370 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png"))
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371 topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
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372 glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
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373 }
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374 filtOut <- makeOut(paste0(deMethod, "_filtcounts.tsv"))
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375 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
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376 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
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377 sessionOut <- makeOut("session_info.txt")
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378
3
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379 # Initialise data for html links and images, data frame with columns Label and
0
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380 # Link
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381 linkData <- data.frame(Label=character(), Link=character(),
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382 stringsAsFactors=FALSE)
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383 imageData <- data.frame(Label=character(), Link=character(),
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384 stringsAsFactors=FALSE)
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385
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386 # Initialise vectors for storage of up/down/neutral regulated counts
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387 upCount <- numeric()
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388 downCount <- numeric()
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389 flatCount <- numeric()
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390
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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391 ################################################################################
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392 ### Data Processing
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diff changeset
393 ################################################################################
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394
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395 # Extract counts and annotation data
3
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396 print("Extracting counts")
0
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397 data <- list()
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398 data$counts <- counts
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399 if (haveAnno) {
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400 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
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401 annoord <- geneanno[match(row.names(counts), geneanno[,1]), ]
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402 data$genes <- annoord
0
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diff changeset
403 } else {
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404 data$genes <- data.frame(GeneID=row.names(counts))
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405 }
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406
8
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407 # Creating naming data
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408 samplenames <- colnames(data$counts)
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409 sampleanno <- data.frame("sampleID"=samplenames, factors)
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diff changeset
410
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411 # Creating colours for the groups
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412 cols <- as.numeric(factors[, 1])
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413 col.group <- palette()[cols]
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414
3
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415 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
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416 # samples. Default is no filtering
0
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417 preFilterCount <- nrow(data$counts)
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418 nsamples <- ncol(data$counts)
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419
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diff changeset
420 if (filtCPM || filtSmpCount || filtTotCount) {
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diff changeset
421
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diff changeset
422 if (filtTotCount) {
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423 keep <- rowSums(data$counts) >= opt$cntReq
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424 } else if (filtSmpCount) {
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425 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
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426 } else if (filtCPM) {
8
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427 myCPM <- cpm(data$counts)
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428 thresh <- myCPM >= opt$cpmReq
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429 keep <- rowSums(thresh) >= opt$sampleReq
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diff changeset
430
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diff changeset
431 if ("c" %in% plots) {
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diff changeset
432 # Plot CPM vs raw counts (to check threshold)
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433 pdf(cpmOutPdf, width=6.5, height=10)
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434 par(mfrow=c(3, 2))
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diff changeset
435 for (i in 1:nsamples) {
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436 plot(data$counts[, i], myCPM[, i], xlim=c(0,50), ylim=c(0,3), main=samplenames[i], xlab="Raw counts", ylab="CPM")
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diff changeset
437 abline(v=10, col="red", lty=2, lwd=2)
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438 abline(h=opt$cpmReq, col=4)
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diff changeset
439 }
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
440 linkName <- "CpmPlots.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
441 linkAddr <- "cpmplots.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
442 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
443 invisible(dev.off())
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
444 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
445 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
446
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
447 data$counts <- data$counts[keep, ]
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
448 data$genes <- data$genes[keep, , drop=FALSE]
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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diff changeset
449
12
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
450 if (wantFilt) {
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
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diff changeset
451 print("Outputting filtered counts")
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
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452 filt_counts <- data.frame(data$genes, data$counts)
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
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diff changeset
453 write.table(filt_counts, file=filtOut, row.names=FALSE, sep="\t", quote=FALSE)
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
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diff changeset
454 linkData <- rbind(linkData, data.frame(Label=paste0(deMethod, "_", "filtcounts.tsv"), Link=paste0(deMethod, "_", "filtcounts.tsv"), stringsAsFactors=FALSE))
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
455 }
81796eb60bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents: 11
diff changeset
456
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
457 # Plot Density
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
458 if ("d" %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
459 # 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
460 png(denOutPng, width=1000, height=500)
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 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
462
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
463 # 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
464 lcpm1 <- cpm(counts, log=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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465 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
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466 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
467 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
468 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
469 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
470 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
471
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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diff changeset
472 # after 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
473 lcpm2 <- cpm(data$counts, log=TRUE)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
474 plot(density(lcpm2[,1]), col=col.group[1], lwd=2, las=2, main="", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
475 title(main="Density Plot: Filtered counts", xlab="Log-cpm")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
476 for (i in 2:nsamples){
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
477 den <- density(lcpm2[, i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
478 lines(den$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
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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 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
482 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
483 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
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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
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
486 # 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
487 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
488 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
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diff changeset
489 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
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diff changeset
490 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
491 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
492 den <- density(lcpm1[, 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
493 lines(den$x, den$y, col=col.group[i], lwd=2)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
494 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
495 plot(density(lcpm2[, 1]), col=col.group[1], lwd=2, las=2, main="", xlab="")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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496 title(main="Density Plot: Filtered counts", xlab="Log-cpm")
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
497 for (i in 2:nsamples){
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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diff changeset
498 den <- density(lcpm2[, i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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diff changeset
499 lines(den$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
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diff changeset
500 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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501 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
502 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
503 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
504 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
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diff changeset
505 invisible(dev.off())
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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diff changeset
506 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
507 }
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
508
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
509 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
510 filteredCount <- preFilterCount-postFilterCount
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
511
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
512 # Generating the DGEList object "y"
3
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513 print("Generating DGEList object")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
514 data$samples <- sampleanno
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
515 data$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
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diff changeset
516 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
517 row.names(data$samples) <- colnames(data$counts)
6
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diff changeset
518 y <- new("DGEList", data)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
519
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
520 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
521 # 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
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diff changeset
522 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
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diff changeset
523 factorList <- sapply(names(factors), pasteListName)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
524 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
525 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
parents: 0
diff changeset
526 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
527 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
528 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
529 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
530 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
parents: 0
diff changeset
531 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
532 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
533
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
534 # Calculating normalising factors
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
535 print("Calculating Normalisation Factors")
11
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
536 logcounts <- y #store for plots
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 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
538
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
539 # Generate contrasts information
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
540 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
541 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
542
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
543 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
544 ### Data Output
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
545 ################################################################################
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
546
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
547 # 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
548 if (opt$normOpt != "none" & "b" %in% plots) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
549 png(boxOutPng, width=1000, height=500)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
550 par(mfrow=c(1,2), mar=c(6,4,2,2)+0.1)
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
551 labels <- colnames(counts)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
552
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
553 lcpm1 <- cpm(y$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
554 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
555 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
556 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
557 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
558 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
559
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
560 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
561 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
562 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
563 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
564 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
565 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
566
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
567 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
568 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
569 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
570 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
571
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
572 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
573 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
574 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
575 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
576 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
577 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
578 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
579 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
580 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
581 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
582 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
583 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
584 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
585 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
586 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
587 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
588 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
589
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
590 # 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
591 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
592 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
593
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
594 # 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
595
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
596 # 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
597 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
598 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
599 }
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 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
602 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
603 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
604 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
605 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
606 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
607 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
608
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
609 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
610 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
611 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
612 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
613
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
614 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
615 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
616 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
617 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
618 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
619 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
620 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
621 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
622 }
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
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
625 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
626 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
627
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
628 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
629 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
630 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
631 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
632 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
633 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
634 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
635 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
636
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(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
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 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
640 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
641 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
642 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
643 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
644 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
645
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
646 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
647 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
648 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
649 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
650 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
651 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
652 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
653 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
654 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
655 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
656 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
657 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
658
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
659 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
660 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
661 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
662 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
663 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
664 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
665 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
666 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
667 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
668 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
669 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
670 }
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
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
672 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
673 # 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
674 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
675 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
676 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
677 for (i in 1:nsamples) {
11
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
678 if (opt$normOpt != "none") {
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
679 plotMD(logcounts, column=i, main=paste(colnames(logcounts)[i], "(before)"))
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
680 abline(h=0, col="red", lty=2, lwd=2)
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
681 }
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
682 plotMD(y, column=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
683 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
684 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
685 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
686 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
687 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
688 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
689 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
690
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
691
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 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
693 # limma-trend approach
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
694 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
695 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
696 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
697 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
698 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
699 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
700 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
701 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
702 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
703 # 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
704 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
705 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
706
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
707 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
708 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
709 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
710 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
711 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
712 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
713
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
714 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
715 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
716 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
717 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
718 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
719 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
720
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
721 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
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 # 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
724 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
725 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
726 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
727 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
728 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
729 # 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
730 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
731 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
732
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
733 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
734 # 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
735 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
736 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
737 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
738 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
739 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
740 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
741
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
742 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
743 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
744 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
745 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
746 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
747 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
748
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
749 # 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
750 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
751 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
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 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
754 # 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
755 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
756 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
757 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
758 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
759 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
760 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
761
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
762 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
763 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
764 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
765 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
766 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
767 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
768
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
769 # 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
770 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
771 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
772
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
773 # 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
774 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
775 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
776 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
777 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
778 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
779
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
780 # 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
781 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
782 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
783 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
784 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
785 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
786 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
787 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
788 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
789
11
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
790 # Save library size info
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
791 if (wantLibinfo) {
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
792 efflibsize <- round(y$samples$lib.size * y$samples$norm.factors)
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
793 libsizeinfo <- cbind(y$samples, EffectiveLibrarySize=efflibsize)
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
794 libsizeinfo$lib.size <- round(libsizeinfo$lib.size)
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
795 names(libsizeinfo)[names(libsizeinfo)=="sampleID"] <- "SampleID"
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
796 names(libsizeinfo)[names(libsizeinfo)=="lib.size"] <- "LibrarySize"
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
797 names(libsizeinfo)[names(libsizeinfo)=="norm.factors"] <- "NormalisationFactor"
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
798 write.table(libsizeinfo, file="libsizeinfo", row.names=FALSE, sep="\t", quote=FALSE)
7e8af58c8052 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents: 10
diff changeset
799 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
800
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
801 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
802
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
803 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
804 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
805 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
806 fit <- treat(fit, lfc=opt$lfcReq, robust=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
807 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
808 fit <- treat(fit, lfc=opt$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
809 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
810 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
811
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
812 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
813 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
814 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
815
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
816 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
817 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
818 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
819 # 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
820 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
821 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
822 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
823
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
824 # 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
825 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
826 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
827 } else{
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
828 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
829 }
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
830 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
831 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
832 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
833 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
834
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
835 # 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
836 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
837 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
838 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
839 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
840 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
841 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
842 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
843 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
844 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
845 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
846
10
e26047c4562d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents: 9
diff changeset
847 # 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
848 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
849 # 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
850 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
851 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
852 Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1],
9
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
853 status=status[, i], sample.cols=col.group,
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
854 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$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
855 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
856 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
857 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
858 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
859 }
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
860
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 # 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
862 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
863 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
864 # 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
865 labels <- fit$genes[, 2]
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
866 } else {
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
867 labels <- fit$genes$GeneID
7
e6a4ff41af6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 6
diff changeset
868 }
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
869 limma::volcanoplot(fit, coef=i,
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
870 main=paste("Volcano Plot:", unmake.names(con)),
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
871 highlight=opt$topgenes,
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
872 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
873 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
874 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
875 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
876 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
877
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
878 # 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
879 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
880 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
881
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
882 # 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
883 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
884 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
885 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
886 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
887
8
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
888 # 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
889 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
890 # 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
891 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
892 highlight=opt$topgenes,
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
893 names=fit$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
894 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
895 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
896 highlight=opt$topgenes,
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
897 names=fit$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
898 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
899
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 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
901 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
902 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
903 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
904 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
905
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
906 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
907 # 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
908 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
909 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
910 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
911 } else {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
912 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
913 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
914 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
915 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
916 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
917 # 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
918 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
919 } else {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
920 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
921 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
922 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
923 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
924 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
925 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
926 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
927 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
928 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
929 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
930 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
931
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
932 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
933 # 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
934 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
935 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
936 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
937
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
938 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
939 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
940 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
941 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
942 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
943 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
944 } else {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
945 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
946 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
947 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
948 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
949 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
950 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
951 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
952 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
953 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
954 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
955 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
956 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
957
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
958 # 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
959 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
960 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
961 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
962 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
963 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
964 } 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
965 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
966 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
967 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
968 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
969 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
970
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
971 # 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
972 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
973 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
974
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
975 # 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
976 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
977 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
978 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
979 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
980 ### HTML Generation
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
981 ################################################################################
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 # 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
984 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
985
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
986 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
987
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
988 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
989 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
990 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
991
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
992 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
993 if (grepl("density|box|mds|mdvol", imageData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
994 HtmlImage(imageData$Link[i], imageData$Label[i], width=1000)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
995 } else if (wantWeight) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
996 HtmlImage(imageData$Link[i], imageData$Label[i], width=1000)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
997 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
998 HtmlImage(imageData$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
999 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1000 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1001
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1002 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
1003
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1004 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
1005 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
1006 TableItem()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1007 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
1008 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
1009 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1010 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
1011 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
1012 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
1013 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
1014 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
1015 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
1016 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1017 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
1018 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1019 cata("</table>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1020
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1021 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
1022 #PDFs
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1023 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
1024 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
1025 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
1026 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1027 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1028
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1029 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
1030 if (grepl("mdplot_", linkData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1031 HtmlLink(linkData$Link[i], linkData$Label[i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1032 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1033 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1034
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1035 for (i in 1:nrow(linkData)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1036 if (grepl("volplot", linkData$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
1037 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
1038 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1039 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1040
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1041 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
1042 if (grepl("heatmap", linkData$Link[i])) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1043 HtmlLink(linkData$Link[i], linkData$Label[i])
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1044 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1045 }
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1046
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1047 for (i in 1:nrow(linkData)) {
00a42b66e522 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents: 7
diff changeset
1048 if (grepl("stripcharts", linkData$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
1049 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
1050 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1051 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1052
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1053 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
1054 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
1055 if (grepl(".tsv", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1056 HtmlLink(linkData$Link[i], linkData$Label[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1057 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1058 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1059
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1060 if (wantRda) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1061 cata("<h4>R Data Object:</h4>\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1062 for (i in 1:nrow(linkData)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1063 if (grepl(".RData", linkData$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
1064 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
1065 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1066 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1067 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1068
9
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1069 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
1070 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
1071 if (grepl("glimma", linkData$Link[i])) {
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1072 HtmlLink(linkData$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
1073 }
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1074 }
4255881bebb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents: 8
diff changeset
1075
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1076 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
1077 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
1078 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
1079 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
1080
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1081 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
1082 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
1083
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1084 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
1085 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
1086 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
1087 "CPM in at least", opt$sampleReq, "samples are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1088 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1089 } else if (filtSmpCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1090 tempStr <- paste("Genes without more than", opt$cntReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1091 "counts in at least", opt$sampleReq, "samples are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1092 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1093 } else if (filtTotCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1094 tempStr <- paste("Genes without more than", opt$cntReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1095 "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
1096 "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
1097 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1098
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1099 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
1100 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
1101 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
1102 "%) 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
1103 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
1104 }
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 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
1106 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
1107 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
1108 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1109 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
1110 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1111 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
1112 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
1113 } 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
1114 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
1115 }
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1116 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
1117 ListItem(paste("Testing significance relative to a fold-change threshold (TREAT) was performed using a threshold of log2 =", opt$lfcReq, "at FDR of", opt$pValReq, "."))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1118 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1119 if (wantRobust) {
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1120 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1121 ListItem("TREAT was used with robust settings (robust=TRUE).")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1122 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1123 ListItem("eBayes was used with robust settings (robust=TRUE).")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
1124 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1125 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1126 if (opt$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
1127 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
1128 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
1129 "of ", opt$pValReq," and exhibit log2-fold-change of at ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1130 "least ", opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1131 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
1132 } else if (opt$pAdjOpt=="holm") {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
1133 tempStr <- paste0("MD Plot highlighted genes are significant at adjusted ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1134 "p-value of ", opt$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
1135 "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
1136 opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1137 ListItem(tempStr)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1138 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1139 } else {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
1140 tempStr <- paste0("MD Plot highlighted genes are significant at p-value ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1141 "of ", opt$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
1142 "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
1143 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
1144 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1145 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
1146
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1147 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
1148
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
1149 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
1150
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1151 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
1152 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
1153 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
1154 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
1155
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1156 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
1157 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
1158 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
1159 }
a330ddf43861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents: 1
diff changeset
1160 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
1161 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1162
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1163 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
1164 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
1165 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
1166 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
1167 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
1168 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1169 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
1170 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1171 cata("</table>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1172
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1173 cit <- character()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1174 link <- character()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1175 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
1176 "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
1177 "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
1178 "\">", "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
1179
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1180 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
1181 "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
1182 "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
1183 "\">", "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
1184
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1185 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
1186
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1187 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
1188 "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
1189 "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
1190 "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
1191
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1192 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
1193 "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
1194 "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
1195 "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
1196 "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
1197 link[1],
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1198 "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
1199 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
1200 "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
1201 "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
1202 "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
1203 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
1204 "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
1205 "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
1206 "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
1207 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
1208 "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
1209 "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
1210 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
1211 "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
1212 "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
1213 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
1214 "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
1215 "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
1216 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
1217 "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
1218 "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
1219 "4288-4297")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1220 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
1221 "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
1222 "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
1223 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
1224 "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
1225 "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
1226 "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
1227 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
1228 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
1229 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
1230 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
1231
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1232 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
1233 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
1234 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
1235 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
1236 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
1237 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
1238 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
1239
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1240 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
1241 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
1242 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
1243 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
1244 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
1245 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
1246 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
1247 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
1248
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1249 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
1250
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1251 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
1252 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
1253 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
1254 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1255 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1256
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1257 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
1258 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
1259 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
1260 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
1261 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
1262 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
1263 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
1264 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
1265 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
1266 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
1267 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
1268
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1269 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
1270 cata("</html>")