fix: List-of-Metrics as Vignette

R/fcn_misc.R

@@ -1206,28 +1206,6 @@ peakWidthOverTime = function(data, RT_bin_width = 2)
   return(retLStats)
 }
 
-#'
-#' Create Html file with list of QC metrics
-#' 
-#' @param outdir Target dir where PTXQC_list-of-metrics_template.html is written
-#' @param outname Filename (without directory)
-#' @return Complete filename of written html file
-#' 
-#' @importFrom rmarkdown render pandoc_available
-#' 
-#' @export
-#' 
-createListOfPTXQCMetrics = function(outdir = getwd(), outname = "PTXQC_list-of-metrics.html")
-{
-  html_template = system.file("./reportTemplate/PTXQC_list-of-metrics_template.Rmd", package="PTXQC")
-  cat(paste0("HTML TEMPLATE: ", html_template, "\n"))
-  ## Rmarkdown: convert to Markdown, and then to HTML (or PDF) ...
-  lst_qcMetrics_ord = getMetricsObjects()
-  filename = file.path(outdir, outname)
-  render(html_template, output_file = filename)
-  return (filename)
-}
-
 #' Get all currently available metrics
 #'  
 #' @param DEBUG_PTXQC Use qc objects from the package (FALSE) or from environment (TRUE/DEBUG)

R/qcMetric_EVD.R

@@ -825,7 +825,7 @@ qcMetric_EVD_Charge =  setRefClass(
       "Charge distribution per Raw file. For typtic digests, peptides of charge 2 
 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant.
 Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can 
-cause a shift (see [http://onlinelibrary.wiley.com/doi/10.1002/mas.21544/abstract](Bittremieux 2017, DOI: 10.1002/mas.21544) ).
+cause a shift (see [Bittremieux 2017, DOI: 10.1002/mas.21544](http://onlinelibrary.wiley.com/doi/10.1002/mas.21544/abstract) ).
 The charge distribution should be similar across Raw files.
 Consistent charge distribution is paramount for comparable 3D-peak intensities across samples.
 
@@ -866,8 +866,7 @@ qcMetric_EVD_IDoverRT =  setRefClass(
 Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is 
 uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of 
 identifications over time indicate potential for LC gradient optimization. 
-See [http://www.ncbi.nlm.nih.gov/pubmed/24700534](Moruz et al., GradientOptimizer: An open-source graphical environment for calculating optimized gradients in reversed-phase
-liquid chromatography, Proteomics, 06/2014; 14) for details.
+See [Moruz 2014, DOI: 10.1002/pmic.201400036](http://www.ncbi.nlm.nih.gov/pubmed/24700534) for details.
 
 Heatmap score [EVD: ID rate over RT]: Scored using 'Uniform' scoring function, i.e. constant receives good score, extreme shapes are bad.
 ",

R/qcMetric_MSMSScans.R

@@ -13,8 +13,7 @@ qcMetric_MSMSScans_TopNoverRT =  setRefClass(
     helpTextTemplate = 
       "TopN over retention time. Similar to ID over RT, this metric reflects the complexity of the sample
 at any point in time. Ideally complexity should be made roughly equal (constant) by choosing a proper (non-linear) LC gradient.
-See [http://www.ncbi.nlm.nih.gov/pubmed/24700534](Moruz et al., GradientOptimizer: An open-source graphical environment for calculating optimized gradients in reversed-phase
-liquid chromatography, Proteomics, 06/2014; 14) for details.
+See [Moruz 2014, DOI: 10.1002/pmic.201400036](http://www.ncbi.nlm.nih.gov/pubmed/24700534) for details.
     
 Heatmap score [MS<sup>2</sup> Scans: TopN over RT]: Rewards uniform (function Uniform) TopN events over time.
 ",

README.md

@@ -8,7 +8,7 @@ PTXQC
 
 ### Latest changes / Change log
 
-  - v0.92.03 - Feb 2018: [List of Metrics][ListOfMetrics] added
+  - v0.92.03 - Feb 2018: Full List of Metrics added as vignette
   - v0.92.02 - Jan 2018: plots and metrics of reporter intensity (iTRAQ, TMT, ...) for labeled MSn experiments 
   - v0.92.01 - Oct 2017: fix issue #41 (partial data error)
   - v0.92.00 - Oct 2017: cleaner R interface; log file for drag'n'drop; fix boxPlots issue (usually for large experiments only);
@@ -47,18 +47,17 @@ you can browse the vignettes using either of these commands within R:
     help(package="PTXQC")
     browseVignettes(package = 'PTXQC')
 
-If you do not want to wait that long, have a look at the ['vignettes' subfolder][3].
-The top part contains a small table with technical gibberish, but the rest is identical to the
-vignettes you would see in R.
+If you do not want to wait that long, you can look at the 
+[latest online vignette at CRAN](https://cran.r-project.org/web/packages/PTXQC/vignettes/)
 
 You will find documentation on
+  - Full List of Quality Metrics with help text
   - Input and Output
   - Report customization
   - (for MaxQuant users) Usage of Drag'n'drop
   - (for R users) code examples in R
 
-For a comprehensive overview on the types of metrics available see [List of Metrics/Plots][ListOfMetrics], 
-which also contains a full description for each metric (as seen in the Help section of a Html report).
+The 'List of Metrics' vignette contains a full description for each metric (as seen in the Help section of a Html report).
 
 ### Installation
 
@@ -141,10 +140,8 @@ The input data is available in the ['inst/examples' subfolder][2].
 
 We recommend to use the most recent PTXQC for the best user experience.
 
-  [ListOfMetrics]: http://htmlpreview.github.io/?https://github.com/cbielow/PTXQC/blob/master/PTXQC_list-of-metrics.html
   [1]: https://github.com/cbielow/PTXQC/tree/master/inst/dragNdrop
   [2]: https://github.com/cbielow/PTXQC/tree/master/inst/examples
-  [3]: https://github.com/cbielow/PTXQC/tree/master/vignettes
   [issuetracker]: https://github.com/cbielow/PTXQC/issues
   [JPR_PTXQC]: https://github.com/cbielow/PTXQC/releases/tag/v0.69.3
   [Ref_VignFAQ]: https://github.com/cbielow/PTXQC/blob/master/vignettes/PTXQC-FAQ.Rmd

vignettes/PTXQC-ListOfMetrics.Rmd

@@ -0,0 +1,85 @@
+---
+title: "List of Metrics"
+author: "Chris Bielow <chris.bielow@fu-berlin.de>"
+date: '`r Sys.Date()`'
+output:
+  html_document:
+    mathjax: null
+    number_sections: yes
+    toc: no
+  pdf_document:
+    toc: no
+vignette: >
+  %\VignetteIndexEntry{List of Metrics}
+  %\VignetteEngine{knitr::rmarkdown}
+  \usepackage[utf8]{inputenc}
+---
+
+
+<!-- the TOC (table of content) would go here, but we create it manually to use this as a vignette
+      - - > use 'toc: no' above to disable the TOC 
+ -->
+
+<a id="TOP"/>
+
+<style type="text/css">
+  p { 
+    padding: 5px 0;
+  }
+
+  .helpText {
+    clear: left;
+  }
+
+</style>
+
+```{r setup, include=TRUE, echo=FALSE, results="asis"}
+## global options
+knitr::opts_chunk$set(echo=FALSE, warning=FALSE, error=FALSE, message=FALSE, fig.width=10)
+
+lst_qcMetrics_ord = PTXQC:::getMetricsObjects()
+
+txt_TOC = "# Table of Contents
+  - [Overview](#Overview)
+  - [Metrics](#Metrics)
+"
+txt_BODY = ""
+for (qcm in lst_qcMetrics_ord)
+{
+  newname = gsub("(.*)\\(.*" , "\\1", gsub("[\\*~%]" , " ", gsub("[\\^\">]" , "", qcm$qcName))) 
+  ## remove weird symbols (to serve as link)
+  newname_lnk = gsub("[^a-zA-Z0-9]", "", newname)
+  txt_TOC = paste0(txt_TOC, paste0("    - [", newname, "](#", newname_lnk, ")\n"))
+  txt_BODY = paste0(txt_BODY, '\n
+## ', newname, ' <a name="', newname_lnk, '"/>
+\n
+  <div class="helpText">', qcm$helpTextTemplate, '</div>
+<p style="text-align: right"><a href="#TOP">-- back to top --</a></p>\n\n')
+}
+
+## print the TOC
+cat(txt_TOC)
+
+```
+
+# Overview <a name="Overview"/>
+
+The following metrics are implemented in PTXQC.<br>
+
+Reasons why metrics might not appear in every report
+
+ * applicable only to certain types of data, e.g. SILAC or TMT
+ * metric was disabled manually using the YAML config file
+ * missing input data (incomplete tables), e.g. only evidence.txt is present
+
+
+Some metrics are incompletely named here, since they might contain (hithero unknown) thresholds.
+
+# Metrics <a name="Metrics"/>
+```{r metrics, echo=FALSE, results="asis"}
+  cat(txt_BODY)
+```
+
+If the above list is empty, the vignette was not compiled (e.g. when viewing on GitHub).
+Please see https://CRAN.R-project.org/package=PTXQC --> Vignettes for a compiled version.
+