This NEWS file mainly serves as a changelog file,
i.e. a list of new features / bugfixes by version number.

Versions uploaded to CRAN are marked with [CRAN].

Glossary:
 'pr' means 'pull request' on GitHub
 'issue' is an issue on GitHub
 
 The respective details can be found by visiting GitHub, e.g. https://github.com/cbielow/PTXQC/pull/124
 for pr #124 (you can use the same URL also for issues, just change the number)

#################################
#########   CHANGELOG  ##########
#################################

[CRAN] v1.1.2 -- 2025/01/08
  - fix handling of MaxQuant DIA data (pr #138)
  - internal housekeeping, mostly fixing ggplot warnings (pr #138)

[CRAN] v1.1.1 -- 2024/03/11
  - compatibility with latest ggplot2 (v. 3.5.0) (pr #135)

[CRAN] v1.1.0 -- 2023/12/16
  - new DDA metric: frequencies of variable modifications per Raw file (pr #134)

[CRAN] v1.00.17 -- 2023/07/05
  - support for the latest rmzqc package

[CRAN] v1.00.17 -- 2023/07/05
  - support for the latest rmzqc package (prepare for export)
  
[CRAN] v1.00.16 -- 2023/05/17
  - add MaxQuant 2.4 support (#130)

[CRAN] v1.00.15 -- 2023/04/23
  - better reporter ion minimum range in violin plot (pr #124)
  - workaround for MQ bug causing negative scan index in msms_scan.txt (issue #128)
  - use 'rmzqc' package to handle mzQC output (prepare for export)

[CRAN] v1.00.14 -- 2022/09/21
  - [FIX] crash when re-running PTX-QC on a txt folder where a (very old) PTX-QC was already run (issue #118)
  - [FIX] msmsScans TopNoverN metric showing invalid data for MaxQuant 2.x (issue #119)
  - [FEATURE] a better plot for TMT/iTRAQ reporter intensity (issue #123)
  - a few minor things (mainly CRAN docs)

[CRAN] v1.00.13 -- 2022/03/22
  - [FIX] Remove dependency 'kableExtra' and use 'htmlTable' package instead

[CRAN] v1.00.12 -- 2021/11/02
  - [FIX] Documentation and cosmetic fixes (pr #109)
  - [FIX/DOC] improved legends and better links in Html reports (pr #111)
  - [FIX] crash on Raw files with only a single MSMS spectrum (pr #112)

[CRAN] v1.00.11 -- 2021/09/28
  - [FEATURE] initial support for mzQC Quality Control output (pr #105)
  - [FEATURE] missed cleavages metric can be computed from evidence.txt now (pr #104)
  - [FIX] MSMSScans metric will crash on exotic data (pr #107)

[CRAN] v1.0.10 -- 2021/05/29
  - [FEATURE] detect if MaxQuant was run with wrong decimal separator (non UK/US locale) (issue #98)
  - [FIX] issue #97 Revive missing MBR metrics (introduced in PTXQC 1.0.9)
  - [FIX] issue #101 Restore full Parameter list showing MaxQuant parameters
  - [FIX] issue #102 Decoy distribution not shown in MS/MS mass error plot

[CRAN] v1.0.9 -- 2021/01/29
  - [FEATURE] allow redirecting console output to file (#94)
  - [FIX] reduce ggplot warnings
  - [FEATURE] mzQC data type support (preliminary; no export yet)


[CRAN] v1.0.8 -- 2020/12/11
  - [FIX] issue #90 Missed Cleavages Plot missing
  - [FIX] issue #91 Wrong score for MSMSScans Intensity

[CRAN] v1.0.7 -- 2020/11/11
  - [FIX] issue #82 cannot open file Rplots.pdf

[CRAN] v1.0.6 -- 2020/09/09
  - [FIX] issue #85 MzTabReader broken (again)

[CRAN] v1.0.5 -- 2020/06/08
  - [FIX] issue #81 MzTabReader broken
  - [FEATURE] remove redundant parameters (#78)

[CRAN] v1.0.4 -- 2020/03/27
  - [FIX] issue #78 duplicate characters in Parameters table
  - [FEATURE] support for labeled data from mzTab (requires OpenMS develop (pre 2.6))

v1.0.3 -- 2020/03/16
  - [FIX] issue #54 create Html report without internet connection
  - [FIX] mzTab input: fix equal number of peptides/proteins for all Raw files (excessive transferred IDs estimate)
  - minor fixes for compatibility with R 4.0.0 (develop)

[CRAN] v1.0.2 -- 2020/02/11
  - minor fixes for CRAN compatibility

[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)

[CRAN] v0.92.5 -- 2019/03/14
  - [FIX] issue #49 (Raw name simplification)

[CRAN] v0.92.4 -- 2019/02/07
  - [FIX] More robust package vignette builds

[CRAN] v0.92.3 -- 2018/02/06
  - [FEATURE] List of Metrics (PTXQC_list-of-metrics.html) added

v0.92.2 -- 2018/01/29
  - [FEATURE] added plots and metrics of reporter intensity (iTRAQ, TMT, ...) for labeled MSn experiments 

v0.92.1 -- 2017/10/18
  - [FIX] issue #41 (partial data problem)
  - [FIX] read/write report problem on Shiny.io


[CRAN] v0.92.0 -- 2017/10/12
  - [FIX] fix an issue where PTXQC would fail when drawing boxPlots (usually for large experiments only)
  - [FEATURE] - cleaner R interface to main report function (allowing to specify custom output files as arguments)
              - a log file is generated when using drag'n'drop;

[CRAN] v0.91.0 -- 2017/10/06
  - [DOC] Extended 'charge' plot html-documentation (linking to Bittremieux 2017, DOI: 10.1002/mas.21544).
  - [FIX] issue #39 (order of barchart items corrected after changes to ggplot package)
          issue #40 (custom contaminant plot error when not all Raw files are affected)

[CRAN] v0.90.0 -- 2017/08/03
  - [FEATURE] Tables are shown as genuine HTML tables in Html-Output
  
[CRAN] v0.82.6 -- 2017/06/09
  - [FIX] Special Contaminants searched by name in protein ID as well (issue #34)

[CRAN] v0.82.5 -- 2017/05/04
  - [FIX] More robust installation instructions for GitHub package (issue #32)

v0.82.4 -- 2017/04/24
  - [FIX] MS/MS fragment intensity plot fixed for MaxQuant 1.2 results (Basepeak Intensity column was renamed, issue #32)

[CRAN] v0.82.3 -- 2017/04/03
  - [FIX] MS/MS fragment plots can deal with 'Unknown' mass analyzer (e.g. from mzXML input)
  - [FIX] .yaml config file is written completely before actual analysis starts

[CRAN] v0.82.2 -- 2017/02/18
  - [FIX] fix Match-between-runs plotting when data is extremely sparse (issue #30)
  - [DOC] improved description of how to customize YAML config
  - [FEATURE] write out preliminary YAML config upon first invocation, enabling the user to disable metrics on failing runs

v0.82.1 -- 2016/11/03
  -  fixes to new Dependent Peptides (DP) plot (issue #28) (added target sites in percent)

v0.82.0 -- 2016/11/01
  -  [METRIC] new Dependent Peptides (DP) plot (issue #28)
     (if DP were enabled in MaxQuant, the Top5 modifications will be displayed;
      this allows to compare samples, but also hints at overlooked variable modifications)

v0.81.0 -- 2016/10/18
  -  [METRIC] new experimental MS/MS intensity metric 
     (scoring the MS/MS TIC vs. base peak, to look for bad ion transmission or fragmentation)

[CRAN] v0.80.14 -- 2016/10/13 
  -  CRAN test fix (make PANDOC optional -- prevents Html reports and Vignettes)

[CRAN] v0.80.13 -- 2016/10/07
  -  minor documentation changes prior to CRAN submission
  
v0.80.12 -- 2016/09/28
  -  bug fixes
      - fix error during in 'PG: Ratio Density' plot when all ratio data is empty (e.g. for blank samples)

v0.80.11 -- 2016/08/11
  -  bug fixes
      - augment fix from v0.80.9 since MaxQuant for finding a MBR reference Raw file

v0.80.10 -- 2016/08/04
  -  automatic detection which txt files are present [only these are used]

v0.80.9 -- 2016/08/02
  - bug fixes
     - MBR-Metric: if more than one RT-reference is found (which can happen for a VERY stable LC), the first is picked
       https://github.com/cbielow/PTXQC/issues/25
  - minor doc improvements     

v0.80.8 -- 2016/07/13
  - bug fixes
     - avoid crash in pre-calibration metric when there is only a single peptide identified in (any) Raw file

v0.80.7 -- 2016/06/09
  - features
     - support for 32bit R for Drag'n'Drop batch file
  - bug fixes
     - fix missing score distribution plots for custom contaminants
     - small documentation improvements
          
v0.80.6 -- 2016/06/06
  - bug fixes
     - fix NA's (empty bars) in MBR ID transfer plot for very sparse Raw files
     - fix crash when plotting EVD aux-plots for Raw files with NO ID's (0% id rate)
      
v0.80.5 -- 2016/04/15
  - bug fixes
      https://github.com/cbielow/PTXQC/issues/23  (EVD: MS/MS Oversampling bug)

v0.80.4 -- 2016/04/11
  - bug fixes
      https://github.com/cbielow/PTXQC/issues/22  (Drag'n'drop of folders with space character)
  
v0.80.3 -- 2016/04/08
  - bug fixes
      https://github.com/cbielow/PTXQC/issues/21
  - Html report will be created prior to PDF file (if both are requested [default])
  - minor doc improvments (Metric help texts in Html report)

v0.80.2 -- 2016/04/04
  - reduce memory footprint (~50% reduction; replacing ddply() with data.table[])

v0.80.1 -- 2016/03/15
  - experimental missing value metric (on peptide level)
    - density plots (showing what intensities are usually missing)
      - includes simple inter-Raw file normalization scheme
    - percentage of missing values (lower is better) -- used for scoring in heatmap
    
v0.80.0 -- 2016/02
  - Report format is by default now Html and PDF (you get two identical reports)
  - Html report includes help texts describing each metric and scoring
  - order of metrics is now matching the wet-lab workflow (roughly), but can be customized (i.e. user-defined) using the YAML config
  - removed Bioconductor dependency (for easier installation)
  - bugfixes / minor improvements

v0.70.3
  - internal restructuring

v0.70.2
  - faster loading of txt files / better consistency checking
  - support for Chinese "NA" entries in Txt files
  
v0.70.1
  - fix empty parameter page (bug in 0.70.0)
  
v0.70.0
  - support for data containing MS3 scans  
