Mercurial > repos > lecorguille > xcms_summary

#!/usr/bin/env Rscript
# version="1.0.0"
#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM


# ----- ARGUMENTS BLACKLIST -----
#xcms.r
argBlacklist=c("zipfile","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf")
#CAMERA.r
argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path")

# ----- PACKAGE -----

pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","CAMERA","batch")
for(pkg in pkgs) {
    cat(pkg,"\n")
    suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
}


# ----- FUNCTION -----
writehtml = function(...) { cat(...,"\n", file=htmlOutput,append = TRUE,sep="") }


# ----- ARGUMENTS -----

listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects


# ----- ARGUMENTS PROCESSING -----

#image is an .RData file necessary to use xset variable given by previous tools
load(listArguments[["image"]]);

htmlOutput = "summary.html"
if (!is.null(listArguments[["htmlOutput"]])) htmlOutput = listArguments[["htmlOutput"]];

user_email = NULL
if (!is.null(listArguments[["user_email"]])) user_email = listArguments[["user_email"]];

# if the RData come from CAMERA
if (!exists("xset") & exists("xa")) xset=xa@xcmsSet

# retrocompatability
if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset)))

if (!exists("xset")) stop("You need at least a xset or a xa object.")


# ----- MAIN PROCESSING INFO -----
writehtml("<!DOCTYPE html>")
writehtml("<HTML lang='en'>")

writehtml("<HEAD>")
    writehtml("<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />")

    writehtml("<title>[W4M] XCMS analysis summary</title>")

    writehtml("<style>")
        writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")
        writehtml("td,th { padding: 5px; padding-right: 12px; }")
        writehtml("th { background: #898989; text-align:left;color: white;}")
        writehtml("h2 { color: #FFA212; }")
        writehtml("ul li { margin-bottom:10px; }")
    writehtml("</style>")
writehtml("</HEAD>")

writehtml("<BODY>")
    writehtml("<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>")
    # to pass the planemo shed_test
    if (user_email != "test@bx.psu.edu") {
        if (!is.null(user_email)) writehtml("By: ",user_email," - ")
        writehtml("Date: ",format(Sys.time(), "%y%m%d-%H:%M:%S"))
    }
    writehtml("</div>")

    writehtml("<h2>Samples used:</h2>")
    writehtml("<div><table>")
        if (all(sampnames(xset) == sampleNamesList$sampleNamesMakeNames)) {
            sampleNameHeaderHtml = paste("<th>sample</th>")
            sampleNameHtml = paste("<td>",sampnames(xset),"</td>")
        } else {
            sampleNameHeaderHtml = paste("<th>sample</th><th>sample renamed</th>")
            sampleNameHtml = paste("<td>",sampnames(xset),"</td><td>",sampleNamesList$sampleNamesMakeNames,"</td>")
        }

        if (!exists("md5sumList")) {
            md5sumHeaderHtml = ""
            md5sumHtml = ""
            md5sumLegend=""
        } else if (is.null(md5sumList$removalBadCharacters)) {
            md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th>")
            md5sumHtml = paste("<td>",md5sumList$origin,"</td>")
            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 chancged during the process."
        } else {
            md5sumHeaderHtml = paste("<th>md5sum<sup>*</sup></th><th>md5sum<sup>**</sup> after bad characters removal</th>")
            md5sumHtml = paste("<td>",md5sumList$origin,"</td><td>",md5sumList$removalBadCharacters,"</td>")
            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 chancged during the process.<br/><sup>**</sup>Because some bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"
        }

        writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")
        writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>"))

    writehtml("</table>")
    writehtml(md5sumLegend)
    writehtml("</div>")

    writehtml("<h2>Function launched:</h2>")
    writehtml("<div><table>")
        writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")
        for(tool in names(listOFlistArguments)) {
            listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]

            timestamp = strsplit(tool,"_")[[1]][1]
            xcmsFunction = strsplit(tool,"_")[[1]][2]
            writehtml("<tr><td rowspan='",length(listOFlistArgumentsDisplay),"'>",timestamp,"</td><td rowspan='",length(listOFlistArgumentsDisplay),"'>",xcmsFunction,"</td>")
            line_begin=""
            for (arg in names(listOFlistArgumentsDisplay)) {
                writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")
                line_begin="<tr>"
            }
        }
    writehtml("</table>")
    writehtml("<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss")
    writehtml("</div>")

    writehtml("<h2>Informations about the xcmsSet object:</h2>")

    writehtml("<div><pre>")
        log_file=file(htmlOutput, open = "at")
        sink(log_file)
        sink(log_file, type = "output")
            xset
        sink()
    writehtml("</pre></div>")

    if (exists("xa")) {
        writehtml("<h2>Informations about the CAMERA object:</h2>")

        writehtml("<div>")
            writehtml("Number of pcgroup: ",length(xa@pspectra))
        writehtml("</div>")
    }

    writehtml("<h2>Citations:</h2>")
    writehtml("<div><ul>")
        writehtml("<li>To cite the <b>XCMS</b> package in publications use:")
            writehtml("<ul>")
            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>")
            writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>")
            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>")
            writehtml("</ul>")
        writehtml("</li>")

        writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")
            writehtml("<ul>")
            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>")
            writehtml("</ul>")
        writehtml("</li>")

        writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")
            writehtml("<ul>")
            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>")
            writehtml("</ul>")
        writehtml("</li>")
    writehtml("</ul></div>")

writehtml("</BODY>")

writehtml("</HTML>")
author	lecorguille
date	Mon, 30 Jan 2017 08:54:06 -0500
parents	ed8d80fc927c
children	27e7da5f6848