Changelog

Source: NEWS.md

ggwas 0.99.2

• Added y_truncate parameter for Manhattan plots with broken y-axis, showing extreme p-values in a compressed zone above the break
• Added snp_density() with heatmap and points styles for SNP density karyograms with centromere markers
• Added density_signal_plot() dual-track comparison of genotyping density vs association signal
• Added chr_info_human(), chr_info_mouse(), chr_info_cattle() for built-in chromosome data, and chr_info_ucsc() for any UCSC assembly
• Used Greek letter on axis labels in volcano and architecture plots
• Reversed color scale in heatmaps (dark = high values)
• Filled empty bins in pvalue_heatmap() to eliminate gaps
• Replaced scattermore with geom_point for correct circle shapes
• Showed legends by default in journal themes
• Reduced overlapping text in genetic correlation and PheWAS plots

ggwas 0.99.1

• Added PheWAS, colocalization, fine-mapping, genetic correlation, and architecture plots
• Added data utilities: filter_region(), maf_filter(), merge_gwas(), get_loci()
• Added scattermore support for faster rendering of large datasets
• Expanded vignette with interpretation guides for all plot types
• Added Zenodo DOI
• Fixed integer overflow in cumulative BP calculation
• Fixed NA handling in highlight_regions()

ggwas 0.99.0

Initial Bioconductor pre-release.

Plot types

• Manhattan plot with smart downsampling, highlighting, and labeling
• QQ plot with confidence bands, genomic inflation factor, and stratification
• Miami plot for two-study comparison
• Locus zoom plot with LD coloring and gene track support
• Genome-wide p-value heatmap (novel)
• Effect-size volcano plot (novel)
• Circular Manhattan with multi-ring support (novel)
• Enrichment Manhattan with functional annotation overlays (novel)
• Multi-trait Manhattan with pleiotropy detection (novel)
• Summary dashboard with automatic panel tags (novel)

Gene annotation

• manhattan_genes() for labeling peaks with gene names
• annotate_genes() for nearest-gene mapping
• top_hits() with clumping and cytoband estimation
• highlight_regions() for marking genomic regions
• Arrow-style annotations

Themes and palettes

• Journal themes: Nature, Science, Cell, PLOS, presentation, poster
• 14 colorblind-safe palettes
• Publication presets via gwas_preset()

Data I/O

• Readers for PLINK, REGENIE, GCTA, GEMMA, and generic formats
• Automatic column name detection
• as_gwas_data() constructor with validation