NEWS

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ribiosPlot 1.3.0 (2026-02-25)

• Initial CRAN submission
• Package prepared for CRAN submission with comprehensive documentation
• Depends on ribiosUtils (on CRAN)
• Optional Vennerable integration for users who install it separately

ribiosPlot 1.1.30

• Add royalredgrayblue and royalbluegrayred color palettes
• plotPCA: xlim/ylim parameters auto-adjust for text labels
• Add function getLims to get xlim/ylim values from vectors

ribiosPlot 1.1.29

• compactPar more flexible to accept and pass parameters to par

ribiosPlot 1.1.28

• Fix bug in heat function: return (n)

ribiosPlot 1.1.26

• Add compactTrellis() and setCompactTrellis() for compact publication figures
• Add function p2asterisk to map p values to asterisk symbols
• Use roxygen2 for documentation

ribiosPlot 1.1.25

• Add function fcbrewer for factor-matching colors
• Improved manual pages
• Rename sqlayout to squareLayout
• Rename compPar to compactPar

ribiosPlot 1.1.24

• biosHeatmap: cex main size better guessed

ribiosPlot 1.1.23

• Add intRange and squareLayout
• pdf2png works on UDIS machine

ribiosPlot 1.1.22

• Add histMat to visualize matrices with histograms
• Add plotPCA

ribiosPlot 1.1.20

• Add qHist and xclipHist histogram functions

ribiosPlot 1.1.19

• Add ribiosUtils to dependency list

ribiosPlot 1.1.18

• Add pdf2png to convert PDF to PNG

ribiosPlot 1.1.17

• Add cyanblackyellow and yellowblackyan color combinations
• Add jitter.xyplot

ribiosPlot 1.1.16

• brewer.pal.factor auto-adjusts color palette size
• PCA plotting functions refactored

ribiosPlot 1.1.15

• Update boxplot.Rscript with improved features

ribiosPlot 1.1.14

• Add idev and ipdf functions for plotting in Rscripts
• Add blackyellowred and blackgoldred color panels

ribiosPlot 1.1.13

• exprs-boxplot.Rscript: accepts tab-delimited and gct files

ribiosPlot 1.1.12

• exprs-boxplot.Rscript works with GCT files

ribiosPlot 1.1.11

• Bug fix: boundNorm works with NAs

ribiosPlot 1.1.10

• Fix typos in brewer.pal.factor and brewer.pal.factorLevels

ribiosPlot 1.1.9

• exprs-boxplot.Rscript: handle user-specified ylim values

ribiosPlot 1.1.8

• Distance function changed from dist to robustDist
• Add documentation for color functions
• Substantially updated biosHeatmap documentation

ribiosPlot 1.1.7

• coverage-plot.Rscript feature file improvements

ribiosPlot 1.1.6

• Add exprs-boxplot.Rscript for command line boxplots

ribiosPlot 1.1.5

• coverage-plot.Rscript supports sequence annotation

ribiosPlot 1.1.4

• Add -featurefile option to coverage-plot.Rscript
• Fix partial matching bug in biosHeatmap

ribiosPlot 1.1.3

• Add coverage-plot.Rscript

ribiosPlot 1.1.2

• biosHeatmap.Rscript uses Ward as default clustering method

ribiosPlot 1.1.1

• geneset_xyplot.Rscript improvements

ribiosPlot 1.1.0

• Add whiteblueblackheat to three-color palettes

ribiosPlot 1.0.9

• Add whiteblack and blackwhite to two-color palettes

ribiosPlot 1.0.8

• Add guessWH function for auto width/height ratio of heatmaps
• Margins automatically determined based on xlab/ylab

ribiosPlot 1.0.7

• biosHeatmap.Rscript: lwids and lheis options obsolete

ribiosPlot 1.0.6

• Data import taken over by ribiosIO::read_exprs_matrix
• Long titles wrapped in biosHeatmap

ribiosPlot 1.0.5

• Add Rscript subdirectory for plotting scripts

ribiosPlot 1.0.4

• Export colorpanel function

ribiosPlot 1.0.3

• Add zlim option to biosHeatmap

ribiosPlot 1.0.2

• Add turyeb color palette

ribiosPlot 1.0.1

• Margins automatically guessed
• Fine tuning of heatmap key plot parameters

ribiosPlot 1.0.0

• Initial release: refactor visualization functions from ribios package