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Merge pull request #3 from bedapub/devel
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‎.github/workflows/standard-ci-workflow.yml‎

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with:
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extra-packages: any::rcmdcheck
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needs: check
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# Skip ribiosArg (not yet on CRAN) and Vennerable (GitHub only)
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dependencies: '"hard"'
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- uses: r-lib/actions/check-r-package@v2
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with:

‎DESCRIPTION‎

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Encoding: UTF-8
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RoxygenNote: 7.3.3
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VignetteBuilder: knitr
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Remotes:
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github::bedapub/ribiosUtils,
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github::bedapub/ribiosArg,
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github::js229/Vennerable

‎NEWS.md‎

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# ribiosPlot 1.3.0
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* Initial CRAN submission
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* Package prepared for CRAN submission with comprehensive documentation
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* Depends on ribiosUtils (on CRAN)
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* Optional Vennerable integration for users who install it separately
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# ribiosPlot 1.1.30 (2015-08-04)
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* Add `royalredgrayblue` and `royalbluegrayred` color palettes
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* `plotPCA`: xlim/ylim parameters auto-adjust for text labels
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* Add function `getLims` to get xlim/ylim values from vectors
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# ribiosPlot 1.1.29 (2015-03-13)
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* `compactPar` more flexible to accept and pass parameters to par
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# ribiosPlot 1.1.28 (2015-02-03)
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* Fix bug in heat function: return (n)
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# ribiosPlot 1.1.26 (2015-01-06)
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* Add `compactTrellis()` and `setCompactTrellis()` for compact publication figures
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* Add function `p2asterisk` to map p values to asterisk symbols
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* Use roxygen2 for documentation
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# ribiosPlot 1.1.25 (2014-07-30)
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* Add function `fcbrewer` for factor-matching colors
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* Improved manual pages
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* Rename `sqlayout` to `squareLayout`
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* Rename `compPar` to `compactPar`
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# ribiosPlot 1.1.24 (2014-07-01)
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* `biosHeatmap`: cex main size better guessed
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# ribiosPlot 1.1.23 (2014-04-28)
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* Add `intRange` and `squareLayout`
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* `pdf2png` works on UDIS machine
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# ribiosPlot 1.1.22 (2014-04-22)
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* Add `histMat` to visualize matrices with histograms
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* Add `plotPCA`
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# ribiosPlot 1.1.20 (2014-01-28)
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* Add `qHist` and `xclipHist` histogram functions
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# ribiosPlot 1.1.19 (2014-01-23)
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* Add ribiosUtils to dependency list
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# ribiosPlot 1.1.18 (2014-01-22)
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* Add `pdf2png` to convert PDF to PNG
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# ribiosPlot 1.1.17 (2013-08-19)
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* Add `cyanblackyellow` and `yellowblackyan` color combinations
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* Add `jitter.xyplot`
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# ribiosPlot 1.1.16 (2013-07-22)
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* `brewer.pal.factor` auto-adjusts color palette size
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* PCA plotting functions refactored
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# ribiosPlot 1.1.15 (2013-02-22)
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* Update boxplot.Rscript with improved features
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# ribiosPlot 1.1.14 (2012-10-20)
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* Add `idev` and `ipdf` functions for plotting in Rscripts
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* Add `blackyellowred` and `blackgoldred` color panels
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# ribiosPlot 1.1.13 (2012-09-11)
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* exprs-boxplot.Rscript: accepts tab-delimited and gct files
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# ribiosPlot 1.1.12 (2012-09-10)
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* exprs-boxplot.Rscript works with GCT files
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# ribiosPlot 1.1.11 (2012-08-22)
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* Bug fix: `boundNorm` works with NAs
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# ribiosPlot 1.1.10 (2012-06-07)
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* Fix typos in `brewer.pal.factor` and `brewer.pal.factorLevels`
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# ribiosPlot 1.1.9 (2012-06-06)
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* exprs-boxplot.Rscript: handle user-specified ylim values
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# ribiosPlot 1.1.8 (2012-05-23)
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* Distance function changed from dist to `robustDist`
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* Add documentation for color functions
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* Substantially updated `biosHeatmap` documentation
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# ribiosPlot 1.1.7 (2012-04-30)
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* coverage-plot.Rscript feature file improvements
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# ribiosPlot 1.1.6 (2012-04-15)
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* Add exprs-boxplot.Rscript for command line boxplots
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# ribiosPlot 1.1.5 (2012-04-02)
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* coverage-plot.Rscript supports sequence annotation
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# ribiosPlot 1.1.4 (2012-03-19)
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* Add -featurefile option to coverage-plot.Rscript
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* Fix partial matching bug in `biosHeatmap`
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# ribiosPlot 1.1.3 (2012-03-09)
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* Add coverage-plot.Rscript
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# ribiosPlot 1.1.2 (2012-02-14)
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* biosHeatmap.Rscript uses Ward as default clustering method
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# ribiosPlot 1.1.1 (2011-12-08)
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* geneset_xyplot.Rscript improvements
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# ribiosPlot 1.1.0 (2011-12-02)
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* Add `whiteblueblackheat` to three-color palettes
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# ribiosPlot 1.0.9 (2011-11-23)
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* Add `whiteblack` and `blackwhite` to two-color palettes
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# ribiosPlot 1.0.8 (2011-11-22)
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* Add `guessWH` function for auto width/height ratio of heatmaps
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* Margins automatically determined based on xlab/ylab
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# ribiosPlot 1.0.7 (2011-11-17)
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* biosHeatmap.Rscript: lwids and lheis options obsolete
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# ribiosPlot 1.0.6 (2011-11-16)
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* Data import taken over by ribiosIO::read_exprs_matrix
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* Long titles wrapped in `biosHeatmap`
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# ribiosPlot 1.0.5 (2011-11-15)
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* Add Rscript subdirectory for plotting scripts
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# ribiosPlot 1.0.4 (2011-11-10)
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* Export `colorpanel` function
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# ribiosPlot 1.0.3 (2011-10-10)
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* Add zlim option to `biosHeatmap`
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# ribiosPlot 1.0.2 (2011-10-05)
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* Add `turyeb` color palette
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# ribiosPlot 1.0.1 (2011-10-04)
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* Margins automatically guessed
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* Fine tuning of heatmap key plot parameters
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# ribiosPlot 1.0.0 (2011-09-20)
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* Initial release: refactor visualization functions from ribios package

‎README.md‎

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*ribiosPlot*: Data transformation and visualisation
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===
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![R-CMD-check badge](https://github.com/bedapub/ribiosPlot/workflows/R-CMD-check/badge.svg)
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## What is *ribiosPlot*?
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*ribiosPlot* is a R package in the *ribios* suite that assists data transformation and visualization.

‎cran-comments.md‎

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## R CMD check results
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0 errors | 0 warnings | 2 notes
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0 errors | 0 warnings | 3 notes
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### Notes explanation
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1. **Unavailable namespace imported from by a ':::' call: 'Vennerable'**
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1. **Suggests or Enhances not in mainstream repositories: ribiosArg, Vennerable**
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- ribiosArg will be submitted to CRAN after ribiosUtils is accepted
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- Vennerable is not on CRAN (maintained on GitHub)
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2. **Unavailable namespace imported from by a ':::' call: 'Vennerable'**
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The package enhances Vennerable (not on CRAN) with a modified Venn diagram
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plotting function. This functionality is optional and protected by
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`if(require("Vennerable"))`. Users who don't have Vennerable installed
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will simply not have access to this single function.
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2. **Possibly unsafe calls: unlockBinding, assignInNamespace**
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3. **Possibly unsafe calls: unlockBinding, assignInNamespace**
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These calls are used solely within the optional `plotVenn()` function to
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patch a layout issue in the Vennerable package. The function is only
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called when Vennerable is available and the user explicitly requests

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