ProTeomiX (PTX) Quality Control (QC) Report"

## 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

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_ord[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')
  }


Try the PTXQC package in your browser

Any scripts or data that you put into this service are public.

PTXQC documentation built on June 2, 2021, 5:07 p.m.