Changelog

Source: NEWS.md

MutGlyph 0.2.0

Plots

• Generic scored annotation tracks can be added to rainfallPlot() and gisticChromPlot(), with shared genomic coordinates and compact, strand-aware gene-body rendering.
• Offline scored gene-body annotations are available for hg18, hg19, and hg38. Popularity scores prioritize labels for navigation; they do not represent biological importance.
• lollipopPlot(), lollipopPlot2(), and rainfallPlot() can hide their autogenerated titles with showTitle = FALSE.
• The package now uses GenomeSpy 0.85.0.

Interaction and output

• Export controls for PNG and SVG are more stable across widget layouts.
• Annotation-rich widgets use compact columnar serialization, including correct handling of one-value transport arrays.

Documentation

• Added a gene annotation guide covering bundled resources, custom tracks, popularity scoring, and use with rainfall and GISTIC plots.
• Improved discovery of the interactive plot guides and examples.

MutGlyph 0.1.0

Initial release.

Plots

• Interactive, maftools-compatible oncoplot(), including mutation and CNV layers, clinical annotations, Ti/Tv, sample and gene summaries, and mean VAF.
• rainfallPlot() with kataegis detection and regional views.
• lollipopPlot() and lollipopPlot2() for single- and two-cohort protein mutation landscapes, with custom domains and annotations.
• gisticChromPlot() for chromosome-wide amplification and deletion landscapes, custom annotations, and regional views.

Interaction and output

• Responsive GenomeSpy widgets with zooming, panning, and tooltips.
• Full-window viewing, JSON specification download, and SVG or PNG export.
• Compact columnar transport for embedded data keeps generated HTML sizes manageable.

Documentation

• Guides for oncoplots, rainfall plots, lollipop plots, and GISTIC plots.
• Reproducible examples based on maftools and TCGA-derived example data.