In cbielow/PTXQC: Quality Report Generation for MaxQuant and mzTab Results

## global options
knitr::opts_chunk$set(echo=FALSE, warning=FALSE, error=FALSE, message=FALSE, fig.width=10)

Overview

Checks

MaxQuant had an english locale (dot as decimal separator; otherwise you would receive an error when generating the report)

(hover here for details)

Dynamic (at this very point in time) check of this system's locale (region) settings
(independent of how the txt-folder for this report was generated!)

Decimal separator:

Quick guide

• navigate using the 'Table of Content' above or just scroll down
• collapse sections by just clicking their name
• click on the "↓ Show Help" symbol to see a description for each metric and its scoring
• edit the YAML config ">r paste0("file:./", basename(rprt_fns$yaml_file)) to
  • set the report format (HTML, plainPDF, or both)
  • disable metrics
  • customize the order of metrics
  • set individual target thresholds
• edit r paste0("file:./", basename(rprt_fns$filename_sorting)) to customize
  • the order of Raw files in plots and heatmap
  • abbreviations of Raw file names
• edit the Html template r paste0("file:./", basename(html_template)) to
  • alter the look and feel of this report (e.g. colors, font and image sizes, help texts, etc.)
• report bugs and file requests via the GitHub issue tracker
• full PTXQC manual available here

HeatMap

hm[["plot"]]

Name Mapping

if(!is.null(pl_nameMapping) && (!any(is.na(pl_nameMapping)))) {
  cat(pl_nameMapping$htmlTable)
}

Metrics

  #for (qcm in lst_qcMetrics[1:3])
  for (qcm in lst_qcMetrics)
  {
    if (length(qcm$plots) == 0) next; # skip empty metrics
    #debug: 
    #cat(c("processing ", qcm$qcName))
    v_titles = qcm$getTitles(subtitle_sep = "\n<b>")
    plots = qcm$getPlots(withTitle = FALSE)
    if (length(v_titles) != length(plots)) {
      ## this is weird...
      stop("Number of titles is unequal to number of plots ...")
    }
    last_title = ""
    for (i in 1:length(v_titles))
    {
      if (last_title != v_titles[i]) {  ## print only new titles
        cat(paste0("\n\n### ", gsub("\n", "\n<br>", v_titles[i]), "</b>\n\n"))
      }
      if (i == 1) { ## print helpText only once
        cat(paste0('\n
<div>
  <div class="helpSymbol">&darr; Show Help</div>
  <div class="helpText">', qcm$helpText, "</div>
</div>"))
      }
      if (!is.na(qcm$htmlTable))
      { ## if there is an HTML table, prefer it over the plots
        cat(qcm$htmlTable)
        break;
      }
      print(plots[[i]])
      cat("\n<br>\n")
      last_title = v_titles[i]
    }
    cat('\n<p style="text-align: right">[back to top](#Overview)</p>\n\n')
  }

cbielow/PTXQC documentation built on March 13, 2024, 5:08 a.m.