Mercurial > repos > lecorguille > xcms_summary

annotate xcms_summary.r @ 29:2a2850fdf29e draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:23:36 +0000
parents 018a9771de28
children
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ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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1 #!/usr/bin/env Rscript
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5 # ----- ARGUMENTS BLACKLIST -----
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6 #xcms.r
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7 argBlacklist <- c("zipfile", "singlefile_galaxyPath", "singlefile_sampleName", "xfunction", "xsetRdataOutput", "sampleMetadataOutput", "ticspdf", "bicspdf", "rplotspdf")
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8 #CAMERA.r
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9 argBlacklist <- c(argBlacklist, "dataMatrixOutput", "variableMetadataOutput", "new_file_path")
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12 # ----- PACKAGE -----
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13 cat("\tSESSION INFO\n")
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15 #Import the different functions
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16 source_local <- function(fname) {
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17 argv <- commandArgs(trailingOnly = FALSE)
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18 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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19 source(paste(base_dir, fname, sep = "/"))
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20 }
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21 source_local("lib.r")
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23 pkgs <- c("CAMERA", "batch")
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24 loadAndDisplayPackages(pkgs)
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25 cat("\n\n")
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28 # ----- FUNCTION -----
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29 writehtml <- function(...) {
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30 cat(..., "\n", file = htmlOutput, append = TRUE, sep = "")
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31 }
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32 writeraw <- function(htmlOutput, object, open = "at") {
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33 log_file <- file(htmlOutput, open = open)
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34 sink(log_file)
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35 sink(log_file, type = "output")
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36 print(object)
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37 sink()
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38 close(log_file)
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39 }
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40 getSampleNames <- function(xobject) {
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41 if (class(xobject) == "xcmsSet")
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42 return(sampnames(xobject))
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43 if (class(xobject) == "XCMSnExp")
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44 return(xobject@phenoData@data$sample_name)
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45 }
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46 getFilePaths <- function(xobject) {
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47 if (class(xobject) == "xcmsSet")
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48 return(xobject@filepaths)
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49 if (class(xobject) == "XCMSnExp")
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50 return(fileNames(xobject))
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51 }
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52 equalParams <- function(param1, param2) {
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53 writeraw("param1.txt", param1, open = "wt")
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54 writeraw("param2.txt", param2, open = "wt")
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55 return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))
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56 }
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59 # ----- ARGUMENTS -----
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60
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61 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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64 # ----- ARGUMENTS PROCESSING -----
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65
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66 #image is an .RData file necessary to use xset variable given by previous tools
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67 load(args$image)
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68
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69 htmlOutput <- "summary.html"
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70 if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput
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72 user_email <- NULL
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73 if (!is.null(args$user_email)) user_email <- args$user_email
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75 # if the RData come from XCMS 1.x
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76 if (exists("xset")) {
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77 xobject <- xset
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78 # retrocompatability
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79 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject)))
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80 }
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81 # if the RData come from CAMERA
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82 if (exists("xa")) {
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83 xobject <- xa@xcmsSet
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84 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name))
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85 }
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86 # if the RData come from XCMS 3.x
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87 if (exists("xdata")) {
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88 xobject <- xdata
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89 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name))
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90 }
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91
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92 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
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95 # ----- MAIN PROCESSING INFO -----
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96 writehtml("<!DOCTYPE html>")
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97 writehtml("<HTML lang='en'>")
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99 writehtml("<HEAD>")
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100 writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")
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101
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102 writehtml("<title>[W4M] XCMS analysis summary</title>")
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104 writehtml("<style>")
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105 writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
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106 writehtml("td, th { padding: 5px; padding-right: 12px; }")
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107 writehtml("th { background: #898989; text-align:left;color: white;}")
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108 writehtml("h2 { color: #FFA212; }")
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109 writehtml("ul li { margin-bottom:10px; }")
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110 writehtml("</style>")
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111 writehtml("</HEAD>")
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112
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113 writehtml("<BODY>")
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114 writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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115 # to pass the planemo shed_test
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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116 if (user_email != "test@bx.psu.edu") {
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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117 if (!is.null(user_email)) writehtml("By: ", user_email, " - ")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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118 writehtml("Date: ", format(Sys.time(), "%y%m%d-%H:%M:%S"))
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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119 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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120 writehtml("</div>")
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121
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122 writehtml("<h2>Samples used:</h2>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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123 writehtml("<div><table>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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124 if (all(getSampleNames(xobject) == sampleNamesList$sampleNamesMakeNames)) {
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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125 sampleNameHeaderHtml <- paste0("<th>sample</th>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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126 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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127 } else {
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128 sampleNameHeaderHtml <- paste0("<th>sample</th><th>sample renamed</th>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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129 sampleNameHtml <- paste0("<td>", getSampleNames(xobject), "</td><td>", sampleNamesList$sampleNamesMakeNames, "</td>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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130 }
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131
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132 if (!exists("md5sumList")) {
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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133 md5sumHeaderHtml <- ""
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134 md5sumHtml <- ""
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135 md5sumLegend <- ""
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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136 } else if (is.null(md5sumList$removalBadCharacters)) {
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137 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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138 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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139 md5sumLegend <- "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process."
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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140 } else {
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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141 md5sumHeaderHtml <- paste0("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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142 md5sumHtml <- paste0("<td>", md5sumList$origin, "</td><td>", md5sumList$removalBadCharacters, "</td>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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143 md5sumLegend <- "<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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144 }
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145
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146 writehtml("<tr>", sampleNameHeaderHtml, "<th>filename</th>", md5sumHeaderHtml, "</tr>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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147 writehtml(paste0("<tr>", sampleNameHtml, "<td>", getFilePaths(xobject), "</td>", md5sumHtml, "</tr>"))
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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148
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149 writehtml("</table>")
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150 writehtml(md5sumLegend)
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151 writehtml("</div>")
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152
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153 writehtml("<h2>Function launched:</h2>")
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154 writehtml("<div><table>")
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155 writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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156 # XCMS 3.x
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157 if (class(xobject) == "XCMSnExp") {
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158 xcmsFunction <- NULL
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159 params <- NULL
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160 for (processHistoryItem in processHistory(xobject)) {
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161 if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem)))
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162 next
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163 timestamp <- processDate(processHistoryItem)
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164 xcmsFunction <- processType(processHistoryItem)
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165 params <- processParam(processHistoryItem)
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166 writehtml("<tr><td>", timestamp, "</td><td>", xcmsFunction, "</td><td colspan='2'><pre>")
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167 writeraw(htmlOutput, params)
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168 writehtml("</pre></td></tr>")
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169 }
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170 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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171 # CAMERA and retrocompatability XCMS 1.x
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172 if (exists("listOFlistArguments")) {
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173 for (tool in names(listOFlistArguments)) {
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174 listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]
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175
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176 timestamp <- strsplit(tool, "_")[[1]][1]
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177 xcmsFunction <- strsplit(tool, "_")[[1]][2]
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178 writehtml("<tr><td rowspan='", length(listOFlistArgumentsDisplay), "'>", timestamp, "</td><td rowspan='", length(listOFlistArgumentsDisplay), "'>", xcmsFunction, "</td>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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179 line_begin <- ""
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180 for (arg in names(listOFlistArgumentsDisplay)) {
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181 writehtml(line_begin, "<td>", arg, "</td><td>", unlist(listOFlistArgumentsDisplay[arg][1]), "</td></tr>")
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182 line_begin <- "<tr>"
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183 }
29
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184 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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185 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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186 writehtml("</table>")
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187 writehtml("<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss")
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188 writehtml("</div>")
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189
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190 if (class(xobject) == "XCMSnExp") {
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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191 writehtml("<h2>Informations about the XCMSnExp object:</h2>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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192 writehtml("<div><pre>")
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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193 writeraw(htmlOutput, xobject)
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194 writehtml("</pre></div>")
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195 }
2a2850fdf29e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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196
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197 writehtml("<h2>Informations about the xcmsSet object:</h2>")
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198
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199 writehtml("<div><pre>")
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200 # Get the legacy xcmsSet object
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201 xset <- getxcmsSetObject(xobject)
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202 writeraw(htmlOutput, xset)
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203 writehtml("</pre></div>")
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204
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205 # CAMERA
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206 if (exists("xa")) {
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207 writehtml("<h2>Informations about the CAMERA object:</h2>")
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208 writehtml("<div>")
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209 writehtml("Number of pcgroup: ", length(xa@pspectra))
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210 writehtml("</div>")
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211 }
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212
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213 writehtml("<h2>Citations:</h2>")
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214 writehtml("<div><ul>")
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215 writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
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216 writehtml("<ul>")
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217 writehtml("<li>", "Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)", "</li>")
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218 writehtml("<li>", "Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)", "</li>")
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219 writehtml("<li>", "H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)", "</li>")
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220 writehtml("</ul>")
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221 writehtml("</li>")
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222
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223 writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
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224 writehtml("<ul>")
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225 writehtml("<li>", "Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)", "</li>")
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226 writehtml("</ul>")
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227 writehtml("</li>")
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228
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229 writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
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230 writehtml("<ul>")
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231 writehtml("<li>", "Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813", "</li>")
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232 writehtml("</ul>")
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233 writehtml("</li>")
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234 writehtml("</ul></div>")
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236 writehtml("</BODY>")
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237
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238 writehtml("</HTML>")