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annotate deseq2.R @ 44:1cb33de18af5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
author iuc
date Tue, 09 Dec 2025 17:43:58 +0000
parents 621ddf5967d2
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1 #!/usr/bin/env Rscript
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3 # A command-line interface to DESeq2 for use with Galaxy
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4 # written by Bjoern Gruening and modified by Michael Love 2016.03.30
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5 #
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6 # This argument is required:
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7 #
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8 # 'factors' a JSON list object from Galaxy
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9 #
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10 # the output file has columns:
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11 #
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12 # baseMean (mean normalized count)
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13 # log2FoldChange (by default a moderated LFC estimate)
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14 # lfcSE (the standard error)
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15 # stat (the Wald statistic)
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16 # pvalue (p-value from comparison of Wald statistic to a standard Normal)
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17 # padj (adjusted p-value, Benjamini Hochberg correction on genes which pass the mean count filter)
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18 #
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19 # the first variable in 'factors' will be the primary factor.
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20 # the levels of the primary factor are used in the order of appearance in factors.
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21 #
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22 # by default, levels in the order A,B,C produces a single comparison of B vs A, to a single file 'outfile'
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23 #
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24 # for the 'many_contrasts' flag, levels in the order A,B,C produces comparisons C vs A, B vs A, C vs B,
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25 # to a number of files using the 'outfile' prefix: 'outfile.condition_C_vs_A' etc.
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26 # all plots will still be sent to a single PDF, named by the arg 'plots', with extra pages.
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27 #
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28 # fit_type is an integer valued argument, with the options from ?estimateDisperions
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29 # 1 "parametric"
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30 # 2 "local"
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31 # 3 "mean"
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33 # setup R error handling to go to stderr
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34 options(show.error.messages = FALSE, error = function() {
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35 cat(geterrmessage(), file = stderr())
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36 q("no", 1, FALSE)
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37 })
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39 library("getopt")
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40 library("tools")
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41 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
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42 args <- commandArgs(trailingOnly = TRUE)
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44 # get options, using the spec as defined by the enclosed list.
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45 # we read the options from the default: commandArgs(TRUE).
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46 spec <- matrix(c(
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47 "quiet", "q", 0, "logical",
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48 "help", "h", 0, "logical",
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49 "cores", "s", 0, "integer",
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50 "batch_factors", "w", 1, "character",
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51 "outfile", "o", 1, "character",
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52 "countsfile", "n", 1, "character",
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53 "sizefactorsfile", "F", 1, "character",
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54 "rlogfile", "r", 1, "character",
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55 "vstfile", "v", 1, "character",
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56 "header", "H", 0, "logical",
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57 "factors", "f", 1, "character",
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58 "files_to_labels", "l", 1, "character",
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59 "plots", "p", 1, "character",
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60 "tximport", "i", 0, "logical",
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61 "txtype", "y", 1, "character",
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62 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF/GFF3 file
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63 "esf", "e", 1, "character",
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64 "fit_type", "t", 1, "integer",
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65 "many_contrasts", "m", 0, "logical",
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66 "outlier_replace_off", "a", 0, "logical",
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67 "outlier_filter_off", "b", 0, "logical",
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68 "auto_mean_filter_off", "c", 0, "logical",
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69 "use_beta_priors", "d", 0, "logical",
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70 "alpha_ma", "A", 1, "numeric",
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71 "prefilter", "P", 0, "logical",
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72 "prefilter_value", "V", 1, "numeric",
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73 "sample_sheet_mode", "S", 0, "logical",
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74 "sample_sheet", "g", 1, "character",
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75 "factor_columns", "j", 1, "character",
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76 "reference_level", "R", 1, "character",
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77 "target_level", "T", 1, "character",
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78 "collection_files", "C", 1, "character",
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79 "custom_design_formula", "D", 0, "logical",
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80 "design_formula", "G", 1, "character",
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81 "contrast_definition", "K", 1, "character"
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82 ), byrow = TRUE, ncol = 4)
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83 opt <- getopt(spec)
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84
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85 # if help was asked for print a friendly message
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86 # and exit with a non-zero error code
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87 if (!is.null(opt$help)) {
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88 cat(getopt(spec, usage = TRUE))
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89 q(status = 1)
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90 }
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91
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92 # enforce the following required arguments
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93 if (is.null(opt$outfile)) {
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94 cat("'outfile' is required\n")
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95 q(status = 1)
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96 }
44
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97 if (is.null(opt$factors) && is.null(opt$sample_sheet_mode)) {
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98 cat("'factors' is required when not using sample_sheet_mode\n")
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99 q(status = 1)
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100 }
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101
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102 verbose <- is.null(opt$quiet)
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103
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104 source_local <- function(fname) {
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105 argv <- commandArgs(trailingOnly = FALSE)
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106 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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107 source(paste(base_dir, fname, sep = "/"))
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108 }
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109
37
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110 source_local("get_deseq_dataset.R")
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111
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112 suppressPackageStartupMessages({
44
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113 library("DESeq2")
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114 library("RColorBrewer")
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115 library("gplots")
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116 })
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117
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118 if (opt$cores > 1) {
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119 library("BiocParallel")
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120 register(MulticoreParam(opt$cores))
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121 parallel <- TRUE
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122 } else {
44
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123 parallel <- FALSE
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124 }
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125
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126 # build or read sample table
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127
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128 trim <- function(x) gsub("^\\s+|\\s+$", "", x)
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129
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130 # switch on if 'factors' was provided:
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131 library("rjson")
44
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132
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133 if (!is.null(opt$sample_sheet_mode)) {
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134 # Sample sheet mode: build factor_list from sample sheet
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135 filenames_to_labels <- fromJSON(opt$files_to_labels)
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136
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137 # Read sample sheet
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138 sample_sheet <- read.table(opt$sample_sheet, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
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139
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140 # Parse collection files
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141 collection_files <- strsplit(opt$collection_files, ",")[[1]]
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142
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143 # First column of sample sheet should contain sample identifiers
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144 sample_id_col <- colnames(sample_sheet)[1]
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145
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146 if (!is.null(opt$custom_design_formula)) {
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147 # Custom design formula mode
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148 # Extract variable names from formula (remove ~, +, *, :, whitespace)
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149 formula_str <- gsub("^~\\s*", "", opt$design_formula)
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150 formula_vars <- unique(trimws(unlist(strsplit(formula_str, "[+*:]"))))
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151
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152 # Validate all variables exist in sample sheet
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153 missing_vars <- setdiff(formula_vars, colnames(sample_sheet))
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154 if (length(missing_vars) > 0) {
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155 cat(paste0("Error: Variables not found in sample sheet: ", paste(missing_vars, collapse = ", "), "\n"))
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156 cat(paste0("Available columns: ", paste(colnames(sample_sheet), collapse = ", "), "\n"))
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157 q(status = 1)
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158 }
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159
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160 # Use all formula variables as factor columns
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161 factor_col_names <- formula_vars
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162 } else {
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163 # Automatic mode: Parse factor columns (comma-separated column numbers, 1-indexed)
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164 factor_col_nums <- as.integer(strsplit(opt$factor_columns, ",")[[1]])
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165 factor_col_names <- colnames(sample_sheet)[factor_col_nums]
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166 }
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167
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168 # Validate sample sheet matches collection before building factor_list
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169 # Get element identifiers from collection
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170 collection_element_ids <- character(length(collection_files))
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171 for (idx in seq_along(collection_files)) {
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172 file <- collection_files[idx]
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173 file_basename <- basename(file)
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174 if (file_basename %in% names(filenames_to_labels)) {
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175 collection_element_ids[idx] <- filenames_to_labels[[file_basename]]
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176 } else {
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177 cat("Error: Sample sheet validation failed\n")
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178 cat(paste0("Collection file '", file_basename, "' does not have a corresponding element identifier.\n"))
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179 cat("This is an internal error - please report this issue.\n")
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180 q(status = 1)
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181 }
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182 }
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183
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184 # Get sample identifiers from sample sheet
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185 sample_sheet_ids <- sample_sheet[[sample_id_col]]
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186
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187 # Check for mismatches
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188 collection_not_in_sheet <- setdiff(collection_element_ids, sample_sheet_ids)
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189 sheet_not_in_collection <- setdiff(sample_sheet_ids, collection_element_ids)
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190
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191 if (length(collection_not_in_sheet) > 0 || length(sheet_not_in_collection) > 0) {
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192 cat("Error: Sample sheet does not match the input collection\n\n")
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193
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194 if (length(collection_not_in_sheet) > 0) {
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195 cat("The following samples are in the collection but NOT in the sample sheet:\n")
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196 for (id in collection_not_in_sheet) {
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197 cat(paste0(" - ", id, "\n"))
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198 }
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199 cat("\n")
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200 }
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201
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202 if (length(sheet_not_in_collection) > 0) {
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203 cat("The following samples are in the sample sheet but NOT in the collection:\n")
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204 for (id in sheet_not_in_collection) {
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205 cat(paste0(" - ", id, "\n"))
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206 }
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207 cat("\n")
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208 }
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209
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210 cat("Please ensure that:\n")
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211 cat(paste0("1. The first column ('", sample_id_col, "') of the sample sheet contains sample identifiers\n"))
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212 cat("2. These identifiers exactly match the element identifiers in your collection\n")
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213 cat("3. All samples in the collection are listed in the sample sheet\n")
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214 cat("4. All samples in the sample sheet exist in the collection\n")
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215 q(status = 1)
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216 }
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217
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218 # Determine which factor will be the primary factor for contrasts
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219 # In custom mode, the primary factor is the last one in the formula (rightmost term)
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220 # In automatic mode, the first selected factor is primary (formula gets reversed)
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221 if (!is.null(opt$custom_design_formula)) {
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222 primary_factor_index <- length(factor_col_names)
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223 } else {
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224 primary_factor_index <- 1
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225 }
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226
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227 # Build factor_list structure
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228 factor_list <- list()
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229 for (i in seq_along(factor_col_names)) {
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230 factor_name <- factor_col_names[i]
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231
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232 # Group files by factor level, preserving the order of first appearance
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233 level_to_files <- list()
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234 level_order <- character(0) # Track order of first appearance
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235 for (file in collection_files) {
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236 element_id <- filenames_to_labels[[basename(file)]]
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237 # Find matching row in sample sheet
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238 matching_row <- which(sample_sheet[[sample_id_col]] == element_id)
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239 if (length(matching_row) > 0) {
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240 level <- sample_sheet[[factor_name]][matching_row[1]]
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241 if (!(level %in% names(level_to_files))) {
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242 level_to_files[[level]] <- character(0)
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243 level_order <- c(level_order, level) # Record order of first appearance
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244 }
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245 level_to_files[[level]] <- c(level_to_files[[level]], file)
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246 }
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247 }
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248
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249 # Get all levels in order of first appearance (not alphabetically sorted)
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250 all_levels <- level_order
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251
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252 # Handle reference and target levels for the primary contrast factor
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253 # In custom mode: this is the LAST factor in the formula
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254 # In automatic mode: this is the FIRST factor selected (formula will be reversed)
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255 if (i == primary_factor_index) {
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256 # This is the primary factor for contrasts: handle reference/target
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257 # Determine reference level
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258 if (!is.null(opt$reference_level) && nchar(opt$reference_level) > 0) {
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259 ref_level <- trim(opt$reference_level)
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260 # Validate that reference level exists
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261 if (!(ref_level %in% all_levels)) {
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262 cat(paste0("Error: Reference level '", ref_level, "' not found in factor '", factor_name, "'. Available levels: ", paste(all_levels, collapse = ", "), "\n"))
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263 q(status = 1)
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264 }
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265 } else {
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266 # Default: use first level encountered in sample sheet as reference
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267 ref_level <- all_levels[1]
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268 }
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269
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270 # Build factor levels with reference first, then others
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271 # This applies to both automatic and custom modes
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272 if (!is.null(opt$target_level) && nchar(opt$target_level) > 0) {
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273 target_level <- trim(opt$target_level)
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274 # Validate that target level exists
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275 if (!(target_level %in% all_levels)) {
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276 cat(paste0("Error: Target level '", target_level, "' not found in factor '", factor_name, "'. Available levels: ", paste(all_levels, collapse = ", "), "\n"))
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277 q(status = 1)
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278 }
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279 # Explicit target: reference first, target second
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280 levels_to_use <- c(ref_level, target_level)
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281 } else {
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282 # Reference first, then others in order of appearance
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283 other_levels <- all_levels[all_levels != ref_level]
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284 levels_to_use <- c(ref_level, other_levels)
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285 # Target is the first non-reference level
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286 target_level <- other_levels[1]
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287 }
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288
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289 # Store reference and target levels for later contrast specification
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290 # This ensures we use the intended levels, not whatever order files happened to be in
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291 primary_ref_level <- ref_level
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292 primary_target_level <- target_level
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293 } else {
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294 # For secondary factors, use all levels in order of appearance
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295 levels_to_use <- all_levels
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296 }
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297
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298 # Build factor structure in the order specified by levels_to_use
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299 # Following standard DESeq2 convention: reference level is first
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300 factor_levels <- list()
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301 for (level in levels_to_use) {
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302 if (level %in% names(level_to_files)) {
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303 level_entry <- list()
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304 level_entry[[level]] <- level_to_files[[level]]
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305 factor_levels[[length(factor_levels) + 1]] <- level_entry
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306 }
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307 }
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308
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309 factor_list[[length(factor_list) + 1]] <- list(factor_name, factor_levels)
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310 }
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311
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312 # Set primary_factor for sample sheet mode
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313 # This is the factor that will be used for contrasts
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314 if (!is.null(opt$custom_design_formula)) {
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315 # Custom mode: primary factor is the last one in the formula (rightmost term)
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316 primary_factor <- factor_col_names[length(factor_col_names)]
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317 } else {
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318 # Automatic mode: primary factor is the first selected factor (formula will be reversed)
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319 primary_factor <- factor_col_names[1]
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320 }
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321
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322 # Parse contrast_definition if in custom mode
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323 if (!is.null(opt$custom_design_formula) && !is.null(opt$contrast_definition) && nchar(opt$contrast_definition) > 0) {
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324 contrast_parts <- strsplit(opt$contrast_definition, ",")[[1]]
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325 if (length(contrast_parts) != 3) {
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326 cat("Error: contrast_definition must be in format 'factor,target,reference'\n")
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327 q(status = 1)
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328 }
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329 custom_contrast <- list(
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330 factor = trim(contrast_parts[1]),
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331 target = trim(contrast_parts[2]),
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332 reference = trim(contrast_parts[3])
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333 )
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334 # Validate the contrast
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335 if (!(custom_contrast$factor %in% factor_col_names)) {
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336 cat(paste0("Error: Contrast factor '", custom_contrast$factor, "' not found in design formula.\n"))
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337 cat(paste0("Available factors: ", paste(factor_col_names, collapse = ", "), "\n"))
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338 q(status = 1)
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339 }
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340 }
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341 } else {
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342 # Original mode: factors provided directly
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343 parser <- newJSONParser()
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344 parser$addData(opt$factors)
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345 factor_list <- parser$getObject()
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346 filenames_to_labels <- fromJSON(opt$files_to_labels)
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347
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348 # For original mode, extract reference and target levels from the first factor
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349 # In original mode: ref=level1 (denominator), target=level2 (numerator) -> log2(level2/level1)
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350 # So we swap the naming to match the contrast direction used below
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351 primary_factor_data <- factor_list[[1]]
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352 primary_levels <- sapply(primary_factor_data[[2]], function(x) names(x))
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353 primary_target_level <- primary_levels[1] # First level becomes "target" for the swap below
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354 primary_ref_level <- if (length(primary_levels) >= 2) primary_levels[2] else primary_levels[1] # Second level becomes "ref"
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355 }
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356
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
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357 factors <- sapply(factor_list, function(x) x[[1]])
44
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358 # For original mode (not sample_sheet_mode), set primary_factor to first factor
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359 # In sample_sheet_mode, it's already set correctly above
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360 if (is.null(opt$sample_sheet_mode)) {
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361 primary_factor <- factors[1]
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362 }
37
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363 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
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364 labs <- unname(unlist(filenames_to_labels[basename(filenames_in)]))
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
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diff changeset
365 sample_table <- data.frame(
44
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366 sample = basename(filenames_in),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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367 filename = filenames_in,
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368 row.names = filenames_in,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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369 stringsAsFactors = FALSE
37
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370 )
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
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diff changeset
371 for (factor in factor_list) {
44
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372 factor_name <- trim(factor[[1]])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
373 sample_table[[factor_name]] <- character(nrow(sample_table))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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374 lvls <- sapply(factor[[2]], function(x) names(x))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
375 for (i in seq_along(factor[[2]])) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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376 files <- factor[[2]][[i]][[1]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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377 sample_table[files, factor_name] <- trim(lvls[i])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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378 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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379 sample_table[[factor_name]] <- factor(sample_table[[factor_name]], levels = lvls)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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380 # Explicitly set the reference level using relevel() for the primary factor in sample_sheet_mode
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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381 # This ensures DESeq2 knows the reference regardless of factor level order
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
382 # In original mode, we don't relevel because the order from factor_list is already correct
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
383 # Note: primary_factor is already set correctly in sample_sheet_mode before we get here
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
384 if (exists("primary_factor") && factor_name == primary_factor && exists("primary_ref_level") && !is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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385 sample_table[[factor_name]] <- relevel(sample_table[[factor_name]], ref = primary_ref_level)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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386 }
17
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387 }
37
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388 rownames(sample_table) <- labs
17
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389
44
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diff changeset
390 # Build design formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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391 if (!is.null(opt$custom_design_formula)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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392 # Custom mode: use user-provided formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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393 design_formula <- as.formula(opt$design_formula)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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394 # In original mode (not sample_sheet), set primary factor to last variable in formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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395 # In sample_sheet_mode, it's already set correctly above
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
396 if (is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
397 primary_factor <- factors[length(factors)]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
398 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
399 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
400 # Automatic mode: build from selected factors
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
401 design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
402 }
17
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iuc
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403
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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diff changeset
404 # these are plots which are made once for each analysis
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
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diff changeset
405 generate_generic_plots <- function(dds, factors) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
406 library("ggplot2")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
407 library("ggrepel")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
408 library("pheatmap")
24
1a34aec44d60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
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diff changeset
409
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
410 rld <- rlog(dds)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
411 p <- plotPCA(rld, intgroup = rev(factors))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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412 print(p + geom_text_repel(aes_string(x = "PC1", y = "PC2", label = factor(colnames(dds))), size = 3) + geom_point())
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
413 dat <- assay(rld)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
414 dists_rl <- dist(t(dat))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
415 mat <- as.matrix(dists_rl)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
416 colors <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
417 pheatmap(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
418 mat,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
419 clustering_distance_rows = dists_rl,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
420 clustering_distance_cols = dists_rl,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
421 col = colors,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
422 main = "Sample-to-sample distances"
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
423 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
424 plotDispEsts(dds, main = "Dispersion estimates")
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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425 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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diff changeset
426
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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diff changeset
427 # these are plots which can be made for each comparison, e.g.
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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428 # once for C vs A and once for B vs A
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diff changeset
429 generate_specific_plots <- function(res, threshold, title_suffix) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
430 use <- res$baseMean > threshold
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
431 if (sum(!use) == 0) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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432 h <- hist(res$pvalue, breaks = 0:50 / 50, plot = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
433 barplot(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
434 height = h$counts,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
435 col = "powderblue",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
436 space = 0,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
437 xlab = "p-values",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
438 ylab = "frequency",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
439 main = paste("Histogram of p-values for", title_suffix)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
440 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
441 text(x = c(0, length(h$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
442 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
443 h1 <- hist(res$pvalue[!use], breaks = 0:50 / 50, plot = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
444 h2 <- hist(res$pvalue[use], breaks = 0:50 / 50, plot = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
445 colori <- c("filtered (low count)" = "khaki", "not filtered" = "powderblue")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
446 barplot(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
447 height = rbind(h1$counts, h2$counts),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
448 beside = FALSE,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
449 col = colori,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
450 space = 0,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
451 xlab = "p-values",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
452 ylab = "frequency",
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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453 main = paste("Histogram of p-values for", title_suffix)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
454 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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455 text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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456 legend("topright", fill = rev(colori), legend = rev(names(colori)), bg = "white")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
457 }
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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diff changeset
458 plotMA(res, main = paste("MA-plot for", title_suffix), ylim = range(res$log2FoldChange, na.rm = TRUE), alpha = opt$alpha_ma)
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459 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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diff changeset
460
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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diff changeset
461 if (verbose) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
462 cat(paste("primary factor:", primary_factor, "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
463 if (length(factors) > 1) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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464 cat(paste("other factors in design:", paste(factors[-length(factors)], collapse = ","), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
465 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
466 cat("\n---------------------\n")
17
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467 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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468
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
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diff changeset
469 dds <- get_deseq_dataset(sample_table, header = opt$header, design_formula = design_formula, tximport = opt$tximport, txtype = opt$txtype, tx2gene = opt$tx2gene)
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
470
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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471 # use/estimate size factors with the chosen method
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472 if (!is.null(opt$esf)) {
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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473 if (opt$esf %in% list("ratio", "poscounts", "iterate")) {
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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474 cat("Calculating size factors de novo\n")
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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475 dds <- estimateSizeFactors(dds, type = opt$esf)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
476 } else {
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
477 sf_table <- read.table(opt$esf)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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478 # Sort the provided size factors just in case the order differs from the input file order.
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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479 merged_table <- merge(sample_table, sf_table, by.x = 0, by.y = 1, sort = FALSE)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
480 sf_values <- as.numeric(unlist(merged_table[5]))
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
481 "sizeFactors"(dds) <- sf_values
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
482
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
483 cat("Using user-provided size factors:\n")
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
484 print(sf_values)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
485 }
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
486 } else {
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
487 cat("No size factor was used\n")
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
488 }
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
489
43
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diff changeset
490
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
491 # estimate size factors for each sample
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
492 # - https://support.bioconductor.org/p/97676/
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
493 if (!is.null(opt$sizefactorsfile)) {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
494 nm <- assays(dds)[["avgTxLength"]]
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
495 if (!is.null(nm)) {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
496 ## Recommended: takes into account tximport data
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
497 cat("\nsize factors for samples: taking tximport data into account\n")
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
498 size_factors <- estimateSizeFactorsForMatrix(counts(dds) / nm)
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
499 } else {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
500 norm_factors <- normalizationFactors(dds)
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
501 if (!is.null(norm_factors)) {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
502 ## In practice, gives same results as above.
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
503 cat("\nsize factors for samples: no tximport data, using derived normalization factors\n")
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
504 size_factors <- estimateSizeFactorsForMatrix(norm_factors)
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
505 } else {
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
506 ## If we have no other information, estimate from raw.
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
507 cat("\nsize factors for samples: no tximport data, no normalization factors, estimating from raw data\n")
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
508 size_factors <- estimateSizeFactorsForMatrix(counts(dds))
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
509 }
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
510 }
42
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
511 write.table(size_factors, file = opt$sizefactorsfile, sep = "\t", col.names = FALSE, quote = FALSE)
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
512 }
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
513
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
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diff changeset
514 apply_batch_factors <- function(dds, batch_factors) {
44
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diff changeset
515 rownames(batch_factors) <- batch_factors$identifier
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
516 batch_factors <- subset(batch_factors, select = -c(identifier, condition))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
517 dds_samples <- colnames(dds)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
518 batch_samples <- rownames(batch_factors)
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diff changeset
519 if (!setequal(batch_samples, dds_samples)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
520 stop("Batch factor names don't correspond to input sample names, check input files")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
521 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
522 dds_data <- colData(dds)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
523 # Merge dds_data with batch_factors using indexes, which are sample names
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
524 # Set sort to False, which maintains the order in dds_data
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
525 reordered_batch <- merge(dds_data, batch_factors, by.x = 0, by.y = 0, sort = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
526 batch_factors <- reordered_batch[, ncol(dds_data):ncol(reordered_batch)]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
527 for (factor in colnames(batch_factors)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
528 dds[[factor]] <- batch_factors[[factor]]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
529 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
530 colnames(dds) <- reordered_batch[, 1]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
531 return(dds)
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diff changeset
532 }
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
533
29
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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diff changeset
534 if (!is.null(opt$batch_factors)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
535 batch_factors <- read.table(opt$batch_factors, sep = "\t", header = TRUE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
536 dds <- apply_batch_factors(dds = dds, batch_factors = batch_factors)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
537 batch_design <- colnames(batch_factors)[-c(1, 2)]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
538
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
539 if (!is.null(opt$custom_design_formula)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
540 # Custom mode: prepend batch factors to user's formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
541 user_formula_rhs <- gsub("^~\\s*", "", opt$design_formula)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
542 design_formula <- as.formula(paste("~", paste(c(batch_design, user_formula_rhs), collapse = " + ")))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
543 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
544 # Automatic mode: prepend batch factors to generated formula
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
545 design_formula <- as.formula(paste("~", paste(c(batch_design, rev(factors)), collapse = " + ")))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
546 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
547 design(dds) <- design_formula
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
548 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
549
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
550 if (verbose) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
551 cat("DESeq2 run information\n\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
552 cat("sample table:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
553 print(sample_table[, -c(1:2), drop = FALSE])
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
554 cat("\ndesign formula:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
555 print(design_formula)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
556 cat("\n\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
557 cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
558 }
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
559
42
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
560 # minimal pre-filtering
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
561 if (!is.null(opt$prefilter)) {
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
562 keep <- rowSums(counts(dds)) >= opt$prefilter_value
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
563 dds <- dds[keep, ]
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
564 }
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
565
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
566 # optional outlier behavior
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
567 if (is.null(opt$outlier_replace_off)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
568 min_rep <- 7
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
569 } else {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
570 min_rep <- Inf
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
571 if (verbose) cat("outlier replacement off\n")
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
572 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
573 if (is.null(opt$outlier_filter_off)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
574 cooks_cutoff <- TRUE
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
575 } else {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
576 cooks_cutoff <- FALSE
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
577 if (verbose) cat("outlier filtering off\n")
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
578 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
579
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
580 # optional automatic mean filtering
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
581 if (is.null(opt$auto_mean_filter_off)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
582 independent_filtering <- TRUE
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
583 } else {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
584 independent_filtering <- FALSE
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
585 if (verbose) cat("automatic filtering on the mean off\n")
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
586 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
587
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
588 # shrinkage of LFCs
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
589 if (is.null(opt$use_beta_priors)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
590 beta_prior <- FALSE
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
591 if (verbose) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
592 cat("Applied default - beta prior off\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
593 }
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
594 } else {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
595 beta_prior <- opt$use_beta_priors
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
596 }
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
597 sprintf("use_beta_prior is set to %s", beta_prior)
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
598
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
599
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
600 # dispersion fit type
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
601 if (is.null(opt$fit_type)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
602 fit_type <- "parametric"
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
603 } else {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
604 fit_type <- c("parametric", "local", "mean")[opt$fit_type]
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
605 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
606
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
607 if (verbose) cat(paste("using disperion fit type:", fit_type, "\n"))
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
608
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
609 # run the analysis
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
610 dds <- DESeq(dds, fitType = fit_type, betaPrior = beta_prior, minReplicatesForReplace = min_rep, parallel = parallel)
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
611
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
612 # create the generic plots and leave the device open
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
613 if (!is.null(opt$plots)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
614 if (verbose) cat("creating plots\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
615 pdf(opt$plots)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
616 generate_generic_plots(dds, factors)
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
617 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
618
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
619 n <- nlevels(colData(dds)[[primary_factor]])
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
620 all_levels <- levels(colData(dds)[[primary_factor]])
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
621
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
622 if (!is.null(opt$countsfile)) {
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
623 normalized_counts <- counts(dds, normalized = TRUE)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
624 write.table(normalized_counts, file = opt$countsfile, sep = "\t", col.names = NA, quote = FALSE)
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
625 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
626
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
627 if (!is.null(opt$rlogfile)) {
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
628 rlog_normalized <- rlogTransformation(dds)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
629 rlog_normalized_mat <- assay(rlog_normalized)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
630 write.table(rlog_normalized_mat, file = opt$rlogfile, sep = "\t", col.names = NA, quote = FALSE)
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
631 }
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
632
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
633 if (!is.null(opt$vstfile)) {
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
634 vst_normalized <- varianceStabilizingTransformation(dds)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
635 vst_normalized_mat <- assay(vst_normalized)
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
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parents: 36
diff changeset
636 write.table(vst_normalized_mat, file = opt$vstfile, sep = "\t", col.names = NA, quote = FALSE)
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
637 }
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
638
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
639
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
640 if (is.null(opt$many_contrasts)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
641 # Single contrast mode
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
642 if (!is.null(opt$custom_design_formula) && exists("custom_contrast")) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
643 # Use explicit custom contrast
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
644 ref <- custom_contrast$reference
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
645 lvl <- custom_contrast$target
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
646 contrast_factor <- custom_contrast$factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
647 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
648 # Default: contrast using stored reference and target levels
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
649 # This ensures we use the intended reference, not whatever order files happened to be in
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
650
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
651 # Check if we have more than 2 levels without explicit target
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
652 if (length(all_levels) > 2 && is.null(opt$target_level)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
653 cat("Error: Multiple factor levels detected without explicit target_level specification.\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
654 cat(paste0("Factor '", primary_factor, "' has ", length(all_levels), " levels: ", paste(all_levels, collapse = ", "), "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
655 cat("Please either:\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
656 cat(" 1. Specify target_level to indicate which level to compare against the reference, or\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
657 cat(" 2. Use many_contrasts mode to compare all levels pairwise\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
658 q(status = 1)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
659 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
660
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
661 # Use stored reference and target levels
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
662 # contrast = c(factor, level1, level2) computes log2(level1 / level2)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
663 # In original mode: variable names were swapped for backward compatibility
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
664 # In sample_sheet_mode: use them directly (ref=denominator, target=numerator)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
665 if (!is.null(opt$sample_sheet_mode)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
666 # Sample sheet mode: use natural order
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
667 ref <- primary_ref_level # Reference is denominator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
668 lvl <- primary_target_level # Target is numerator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
669 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
670 # Original mode: swap for backward compatibility
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
671 ref <- primary_target_level # This becomes the denominator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
672 lvl <- primary_ref_level # This becomes the numerator
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
673 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
674 contrast_factor <- primary_factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
675 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
676
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
677 res <- results(
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
678 dds,
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
679 contrast = c(contrast_factor, lvl, ref),
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
680 cooksCutoff = cooks_cutoff,
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
681 independentFiltering = independent_filtering
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
682 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
683 if (verbose) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
684 cat("summary of results\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
685 cat(paste0(contrast_factor, ": ", lvl, " vs ", ref, "\n"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
686 print(summary(res))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
687 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
688 res_sorted <- res[order(res$padj), ]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
689 out_df <- as.data.frame(res_sorted)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
690 out_df$geneID <- rownames(out_df) # nolint
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
691 out_df <- out_df[, c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
692 filename <- opt$outfile
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
693 write.table(out_df, file = filename, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
694 if (independent_filtering) {
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
695 threshold <- unname(attr(res, "filterThreshold"))
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
696 } else {
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
697 threshold <- 0
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
698 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
699 title_suffix <- paste0(primary_factor, ": ", lvl, " vs ", ref)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
700 if (!is.null(opt$plots)) {
37
951876579237 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 36
diff changeset
701 generate_specific_plots(res, threshold, title_suffix)
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
702 }
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
703 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
704 # rotate through the possible contrasts of the primary factor
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
705 # write out a sorted table of results with the contrast as a suffix
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
706 # add contrast specific plots to the device
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
707 for (i in seq_len(n - 1)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
708 ref <- all_levels[i]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
709 contrast_levels <- all_levels[(i + 1):n]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
710 for (lvl in contrast_levels) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
711 res <- results(
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
712 dds,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
713 contrast = c(primary_factor, lvl, ref),
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
714 cooksCutoff = cooks_cutoff,
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
715 independentFiltering = independent_filtering
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
716 )
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
717 res_sorted <- res[order(res$padj), ]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
718 out_df <- as.data.frame(res_sorted)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
719 out_df$geneID <- rownames(out_df) # nolint
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
720 out_df <- out_df[, c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
721 filename <- paste0(primary_factor, "_", lvl, "_vs_", ref)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
722 write.table(out_df, file = filename, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
723 if (independent_filtering) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
724 threshold <- unname(attr(res, "filterThreshold"))
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
725 } else {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
726 threshold <- 0
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
727 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
728 title_suffix <- paste0(primary_factor, ": ", lvl, " vs ", ref)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
729 if (!is.null(opt$plots)) {
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
730 generate_specific_plots(res, threshold, title_suffix)
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
731 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
732 }
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
733 }
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
734 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
735
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
736 # close the plot device
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
737 if (!is.null(opt$plots)) {
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
738 cat("closing plot device\n")
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
739 dev.off()
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
740 }
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
741
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
742 cat("Session information:\n\n")
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
743
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents:
diff changeset
744 sessionInfo()