Merge pull request #69 from cbielow/mzTab_support

[FEATURE] v1.0.0: introducing MzTab support and many more. See Changelog for V1.0.0

DESCRIPTION

@@ -1,37 +1,36 @@
 Package: PTXQC
 Type: Package
-Title: Quality Report Generation for MaxQuant Results
-Version: 0.92.6
-Date: 2019-04-16
+Title: Quality Report Generation for MaxQuant and mzTab Results
+Version: 1.0.0
+Date: 2020-01-08
 Author: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
 Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
 Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the 
-             MaxQuant software suite.
+             MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
              Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
-             Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) 'doi:10.1021/acs.jproteome.5b00780'.
+             Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
+             <doi:10.1021/acs.jproteome.5b00780>.
 SystemRequirements: pandoc (http://pandoc.org) for building Vignettes and output reports as HTML 
 Depends:
-    R (>= 3.0.0)
+    R (>= 3.3.0)
 Imports:
     data.table,
     ggplot2 (>= 2.2),
     ggdendro,
-    graphics,
     grid,
-    gridExtra,
     grDevices,
     gtable,
     kableExtra,
     knitr (>= 1.10),
     methods,
     plyr,
-    proto,
     RColorBrewer,
     reshape2,
     rmarkdown,
     seqinr,
     stats,
     utils,
+    UpSetR,
     yaml
 Suggests:
     testthat

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(print,PTXQC_table)
+export(FilenameMapper)
 export(LCS)
 export(LCSn)
 export(RTalignmentTree)
@@ -50,6 +51,7 @@ export(plot_MissedCleavages)
 export(plot_RTPeakWidth)
 export(plot_RatiosPG)
 export(plot_ScanIDRate)
+export(plot_TIC)
 export(plot_TopN)
 export(plot_TopNoverRT)
 export(plot_UncalibratedMSErr)
@@ -70,49 +72,24 @@ export(shortenStrings)
 export(simplifyNames)
 export(supCount)
 export(theme_blank)
+exportClasses(FilenameMapper)
 exportClasses(YAMLClass)
 exportClasses(qcMetric)
+import(RColorBrewer)
+import(UpSetR)
+import(data.table)
 import(ggdendro)
 import(ggplot2)
-import(graphics)
-import(gridExtra)
+import(grDevices)
+import(grid)
 import(gtable)
 import(kableExtra)
+import(knitr)
 import(methods)
-import(proto)
+import(plyr)
+import(reshape2, except = c(dcast, melt))
+import(rmarkdown)
 import(stats)
 import(utils)
-importFrom(RColorBrewer,brewer.pal)
-importFrom(RColorBrewer,brewer.pal.info)
-importFrom(data.table,as.data.table)
-importFrom(data.table,setkey)
-importFrom(grDevices,boxplot.stats)
-importFrom(grDevices,dev.off)
-importFrom(grDevices,pdf)
-importFrom(grid,gList)
-importFrom(grid,gTree)
-importFrom(grid,gpar)
-importFrom(grid,grid.draw)
-importFrom(grid,grid.newpage)
-importFrom(grid,grobHeight)
-importFrom(grid,grobWidth)
-importFrom(grid,rectGrob)
-importFrom(grid,textGrob)
-importFrom(grid,unit.c)
-importFrom(knitr,kable)
-importFrom(plyr,adply)
-importFrom(plyr,compact)
-importFrom(plyr,ddply)
-importFrom(plyr,dlply)
-importFrom(plyr,empty)
-importFrom(plyr,ldply)
-importFrom(plyr,llply)
-importFrom(plyr,mapvalues)
-importFrom(plyr,summarise)
-importFrom(plyr,summarize)
-importFrom(reshape2,dcast)
-importFrom(reshape2,melt)
-importFrom(rmarkdown,pandoc_available)
-importFrom(rmarkdown,render)
+import(yaml)
 importFrom(seqinr,circle)
-importFrom(yaml,as.yaml)

NEWS

@@ -7,6 +7,13 @@ Versions uploaded to CRAN are marked with [CRAN].
 #########   CHANGELOG  ##########
 #################################
 
+[CRAN] v1.0.0 -- 2020/01/08
+  - [FEATURE] support for mzTab input data (e.g. from OpenMS 2.5 'QualityControl' tool)
+  - [FEATURE] new metric: UpSetR plots (shows common sets of peptides across Raw files)
+  - [FEATURE] new metric: Total Ion Count (TIC) plots (for OpenMS' mzTab input only; not supported for MaxQuant)
+  - [FIX] issue #55 (MS2 Calibration metric crash when no evidence is given)
+  - [FIX] issue #56 package data.table not properly imported
+
 [CRAN] v0.92.6 -- 2019/03/14
   - [FIX] issue #51 (crash on MSMSScans)
   - [FIX] issue #54 (timsTOF data fix)