NEWS

ggwas 0.99.10

Add value_manhattan() to plot any per-feature value (rankings, effect sizes, scores) along the genome in Manhattan style.
Add annotate_positions() to map Ensembl gene IDs or symbols to genome coordinates from a GTF, bundled data, biomaRt, or an EnsDb.
value_manhattan() can look up coordinates from a gene-ID column directly via annotate and id.
Bundled gene annotations now include an Ensembl gene_id column.

Chromosome colours now follow the chromosomes present in the data instead of assuming the human set of 26. Manhattan, Miami and volcano plots of non-human genomes (for example cattle, with 29 autosomes plus X) no longer leave the extra chromosomes uncoloured. scale_color_chromosome(), scale_fill_chromosome(), scale_color_gwas() and scale_fill_gwas() gain a chromosomes argument for the same reason.

Point labels now sit in the empty part of the plot with a connector line down to the variant, instead of landing on the points. Manhattan labels go into the headroom above the peaks; trumpet and volcano labels move off the dense band

SNP and gene labels across all plots now share one repel style, so they spread out, always keep a connector line, and stay off the points
Manhattan plots leave headroom at the top, giving top-hit labels room to sit
The summary dashboard top-hits table no longer clips its bottom rows

manhattan_plot() with a single y_truncate value now keeps the peaks above the break and compresses them, instead of dropping everything up to the top
The summary dashboard top-hits table shows the base-pair position again (it was printing NULL)

trumpet_plot(), forest_plot() and effect_compare_plot() match column names case-insensitively, like as_gwas_data()

Column auto-detection is now case-insensitive, so lowercase headers (pos, #chrom, alt, ...) are recognized
-log10(p) columns (LOG10P, neg_log_pvalue, ...) are auto-detected and back-transformed
Fixed a crash when more than one required column could not be detected; the error now lists the missing columns

Added GRanges interoperability: as_granges() exports results to a Bioconductor GRanges, and as_gwas_data() now accepts GRanges input
Added trumpet_plot(): effect size versus minor allele frequency with statistical-power contours showing which variants a study can detect
Added forest_plot() for effect estimates with confidence intervals across cohorts or lead variants
Added effect_compare_plot() comparing variant effects between two studies on their shared variants
Added gene_annotation() with bundled protein-coding genes for GRCh37 and GRCh38, so regional and gene-labelled plots work without a GTF
gene_track() now renders full exon structure when given exon_data
Sped up smart_downsample() with exponential-key weighted sampling

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

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()

Initial Bioconductor pre-release.