{
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  "Package": "ggwas",
  "Title": "Modern 'ggplot2' Visualizations for Genome-Wide Association\nStudies",
  "Version": "0.99.10",
  "Authors@R": "person(\"Bartosz\", \"Czech\", email = \"bartosz.w.czech@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9908-3007\"))",
  "Description": "Create publication-ready visualizations for genome-wide\nassociation studies. Provides 21 plot types including\nManhattan, value Manhattan, QQ, Miami, locus zoom, PheWAS,\ncolocalization, fine-mapping, genetic correlation, SNP density,\nand density-signal comparison plots. Reads PLINK, REGENIE,\nGCTA, and GEMMA formats natively. All plot functions return\n'ggplot2' objects for full customization. Smart downsampling\nhandles datasets with 10 million+ variants.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/bczech/ggwas, https://bczech.github.io/ggwas/",
  "BugReports": "https://github.com/bczech/ggwas/issues",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "biocViews": "Visualization, GenomeWideAssociation, Annotation,\nDataImport, Software",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.0.0",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-10-03 21:23:29 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/ggwas",
  "RemoteRef": "HEAD",
  "RemoteSha": "cb0c15f82f87593116c6a613ea8c1c986666cae9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-04 00:55:06 UTC",
    "User": "root"
  },
  "Author": "Bartosz Czech [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9908-3007>)",
  "Maintainer": "Bartosz Czech <bartosz.w.czech@gmail.com>",
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  "_type": "src",
  "_file": "ggwas_0.99.10.tar.gz",
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  "_created": "2026-10-04T00:55:06.000Z",
  "_published": "2026-10-04T01:01:26.721Z",
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    "note": 7
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37166143994",
  "_status": "success",
  "_upstream": "https://github.com/BiocStaging/ggwas",
  "_commit": {
    "id": "cb0c15f82f87593116c6a613ea8c1c986666cae9",
    "author": "Bartek <32614650+bczech@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "feat: add value_manhattan() and map gene IDs to coordinates (#1)",
    "time": 1791062609
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  "_maintainer": {
    "name": "Bartosz Czech",
    "email": "bartosz.w.czech@gmail.com",
    "login": "bczech",
    "description": " PhD in Biological Sciences 🧬 | Computational biologist | NGS · multi-omics | R/Shiny & R package developer",
    "uuid": 32614650,
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    {
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    {
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  "_tags": [],
  "_topics": [
    "visualization",
    "genomewideassociation",
    "annotation",
    "dataimport",
    "software"
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  "_devurl": "https://github.com/bczech/ggwas",
  "_pkgdown": "https://bczech.github.io/ggwas/",
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.json",
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    "extra/NEWS.txt",
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    "extra/readme.md",
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  ],
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  "_exports": [
    "annotate_genes",
    "annotate_positions",
    "architecture_plot",
    "as_granges",
    "as_gwas_data",
    "calc_lambda",
    "chr_info_cattle",
    "chr_info_human",
    "chr_info_mouse",
    "chr_info_ucsc",
    "circular_manhattan",
    "coloc_plot",
    "density_signal_plot",
    "effect_compare_plot",
    "enrichment_manhattan",
    "filter_region",
    "finemapping_plot",
    "forest_plot",
    "gene_annotation",
    "gene_track",
    "genetic_correlation",
    "get_loci",
    "gwas_palette",
    "gwas_palettes",
    "gwas_preset",
    "gwas_summary",
    "highlight_regions",
    "locus_plot",
    "maf_filter",
    "manhattan_genes",
    "manhattan_plot",
    "merge_gwas",
    "miami_plot",
    "multitrait_manhattan",
    "phewas_plot",
    "pvalue_heatmap",
    "qq_plot",
    "read_gcta_mlma",
    "read_gemma",
    "read_gtf",
    "read_gwas_table",
    "read_plink_assoc",
    "read_plink_linear",
    "read_plink_logistic",
    "read_regenie",
    "scale_color_chromosome",
    "scale_color_gwas",
    "scale_fill_chromosome",
    "scale_fill_gwas",
    "set_sex_chr_map",
    "snp_density",
    "theme_cell",
    "theme_gwas",
    "theme_nature",
    "theme_plos",
    "theme_poster",
    "theme_presentation",
    "theme_science",
    "top_hits",
    "trumpet_plot",
    "validate_gwas_data",
    "value_manhattan",
    "volcano_plot"
  ],
  "_datasets": [
    {
      "name": "example_gwas",
      "title": "Example GWAS dataset",
      "object": "example_gwas",
      "class": [
        "gwas_data",
        "data.frame"
      ],
      "fields": [
        "CHR",
        "BP",
        "SNP",
        "P",
        "BETA",
        "SE",
        "A1",
        "A2",
        "AF"
      ],
      "rows": 8000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "annotate_genes",
      "title": "Annotate peaks with nearest gene names",
      "topics": [
        "annotate_genes"
      ]
    },
    {
      "page": "annotate_positions",
      "title": "Map gene IDs or symbols to genome coordinates",
      "topics": [
        "annotate_positions"
      ]
    },
    {
      "page": "architecture_plot",
      "title": "Genetic architecture plot",
      "topics": [
        "architecture_plot"
      ]
    },
    {
      "page": "as_granges",
      "title": "Convert GWAS results to a GRanges object",
      "topics": [
        "as_granges"
      ]
    },
    {
      "page": "as_gwas_data",
      "title": "Create a gwas_data object",
      "topics": [
        "as_gwas_data"
      ]
    },
    {
      "page": "calc_lambda",
      "title": "Calculate genomic inflation factor (lambda GC)",
      "topics": [
        "calc_lambda"
      ]
    },
    {
      "page": "chr_info",
      "title": "Chromosome information for common species",
      "topics": [
        "chr_info",
        "chr_info_cattle",
        "chr_info_human",
        "chr_info_mouse"
      ]
    },
    {
      "page": "chr_info_ucsc",
      "title": "Fetch chromosome information from UCSC",
      "topics": [
        "chr_info_ucsc"
      ]
    },
    {
      "page": "circular_manhattan",
      "title": "Circular Manhattan plot",
      "topics": [
        "circular_manhattan"
      ]
    },
    {
      "page": "coloc_plot",
      "title": "Colocalization locus plot",
      "topics": [
        "coloc_plot"
      ]
    },
    {
      "page": "density_signal_plot",
      "title": "Density-signal dual-track plot",
      "topics": [
        "density_signal_plot"
      ]
    },
    {
      "page": "effect_compare_plot",
      "title": "Compare variant effects between two GWAS",
      "topics": [
        "effect_compare_plot"
      ]
    },
    {
      "page": "enrichment_manhattan",
      "title": "Enrichment Manhattan plot",
      "topics": [
        "enrichment_manhattan"
      ]
    },
    {
      "page": "example_gwas",
      "title": "Example GWAS dataset",
      "topics": [
        "example_gwas"
      ]
    },
    {
      "page": "filter_region",
      "title": "Filter variants by genomic region",
      "topics": [
        "filter_region"
      ]
    },
    {
      "page": "finemapping_plot",
      "title": "Fine-mapping credible set plot",
      "topics": [
        "finemapping_plot"
      ]
    },
    {
      "page": "forest_plot",
      "title": "Forest plot of effect estimates",
      "topics": [
        "forest_plot"
      ]
    },
    {
      "page": "gene_annotation",
      "title": "Built-in protein-coding gene annotations",
      "topics": [
        "gene_annotation"
      ]
    },
    {
      "page": "gene_track",
      "title": "Gene annotation track",
      "topics": [
        "gene_track"
      ]
    },
    {
      "page": "genetic_correlation",
      "title": "Genetic correlation matrix",
      "topics": [
        "genetic_correlation"
      ]
    },
    {
      "page": "get_loci",
      "title": "Get significant loci",
      "topics": [
        "get_loci"
      ]
    },
    {
      "page": "gwas_palette",
      "title": "GWAS Color Palettes",
      "topics": [
        "gwas_palette"
      ]
    },
    {
      "page": "gwas_palettes",
      "title": "List available GWAS palettes",
      "topics": [
        "gwas_palettes"
      ]
    },
    {
      "page": "gwas_preset",
      "title": "GWAS plot presets",
      "topics": [
        "gwas_preset"
      ]
    },
    {
      "page": "gwas_summary",
      "title": "GWAS Summary Panel",
      "topics": [
        "gwas_summary"
      ]
    },
    {
      "page": "highlight_regions",
      "title": "Add highlighted regions to a Manhattan plot",
      "topics": [
        "highlight_regions"
      ]
    },
    {
      "page": "journal_themes",
      "title": "Journal-specific themes for GWAS plots",
      "topics": [
        "journal_themes",
        "theme_cell",
        "theme_nature",
        "theme_plos",
        "theme_poster",
        "theme_presentation",
        "theme_science"
      ]
    },
    {
      "page": "locus_plot",
      "title": "Locus zoom plot",
      "topics": [
        "locus_plot"
      ]
    },
    {
      "page": "maf_filter",
      "title": "Filter variants by minor allele frequency",
      "topics": [
        "maf_filter"
      ]
    },
    {
      "page": "manhattan_genes",
      "title": "Add gene labels to a Manhattan plot",
      "topics": [
        "manhattan_genes"
      ]
    },
    {
      "page": "manhattan_plot",
      "title": "Manhattan plot",
      "topics": [
        "manhattan_plot"
      ]
    },
    {
      "page": "merge_gwas",
      "title": "Merge multiple GWAS datasets",
      "topics": [
        "merge_gwas"
      ]
    },
    {
      "page": "miami_plot",
      "title": "Miami plot (mirrored Manhattan)",
      "topics": [
        "miami_plot"
      ]
    },
    {
      "page": "multitrait_manhattan",
      "title": "Multi-trait Manhattan plot",
      "topics": [
        "multitrait_manhattan"
      ]
    },
    {
      "page": "phewas_plot",
      "title": "PheWAS plot",
      "topics": [
        "phewas_plot"
      ]
    },
    {
      "page": "pvalue_heatmap",
      "title": "Genome-wide p-value heatmap",
      "topics": [
        "pvalue_heatmap"
      ]
    },
    {
      "page": "qq_plot",
      "title": "QQ plot for GWAS p-values",
      "topics": [
        "qq_plot"
      ]
    },
    {
      "page": "read_gcta_mlma",
      "title": "Read GCTA MLMA results",
      "topics": [
        "read_gcta_mlma"
      ]
    },
    {
      "page": "read_gemma",
      "title": "Read GEMMA association results",
      "topics": [
        "read_gemma"
      ]
    },
    {
      "page": "read_gtf",
      "title": "Read gene annotations from GTF/GFF3 file",
      "topics": [
        "read_gtf"
      ]
    },
    {
      "page": "read_gwas_table",
      "title": "Read GWAS summary statistics from any tabular file",
      "topics": [
        "read_gwas_table"
      ]
    },
    {
      "page": "read_plink_assoc",
      "title": "Read PLINK association results",
      "topics": [
        "read_plink_assoc"
      ]
    },
    {
      "page": "read_plink_linear",
      "title": "Read PLINK linear regression results",
      "topics": [
        "read_plink_linear"
      ]
    },
    {
      "page": "read_plink_logistic",
      "title": "Read PLINK logistic regression results",
      "topics": [
        "read_plink_logistic"
      ]
    },
    {
      "page": "read_regenie",
      "title": "Read REGENIE results",
      "topics": [
        "read_regenie"
      ]
    },
    {
      "page": "scale_color_chromosome",
      "title": "Chromosome color scale",
      "topics": [
        "scale_color_chromosome",
        "scale_fill_chromosome"
      ]
    },
    {
      "page": "scale_color_gwas",
      "title": "Colorblind-safe chromosome color scale",
      "topics": [
        "scale_color_gwas",
        "scale_fill_gwas"
      ]
    },
    {
      "page": "set_sex_chr_map",
      "title": "Configure sex chromosome mapping",
      "topics": [
        "set_sex_chr_map"
      ]
    },
    {
      "page": "snp_density",
      "title": "SNP density karyogram",
      "topics": [
        "snp_density"
      ]
    },
    {
      "page": "theme_gwas",
      "title": "Minimal GWAS theme for ggplot2",
      "topics": [
        "theme_gwas"
      ]
    },
    {
      "page": "top_hits",
      "title": "Extract top hits from GWAS results",
      "topics": [
        "top_hits"
      ]
    },
    {
      "page": "trumpet_plot",
      "title": "Trumpet plot: effect size versus allele frequency with power contours",
      "topics": [
        "trumpet_plot"
      ]
    },
    {
      "page": "validate_gwas_data",
      "title": "Validate a gwas_data object",
      "topics": [
        "validate_gwas_data"
      ]
    },
    {
      "page": "value_manhattan",
      "title": "Manhattan plot of an arbitrary per-feature value",
      "topics": [
        "value_manhattan"
      ]
    },
    {
      "page": "volcano_plot",
      "title": "GWAS effect-size volcano plot",
      "topics": [
        "volcano_plot"
      ]
    }
  ],
  "_pkglogo": "https://github.com/BiocStaging/ggwas/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/BiocStaging/ggwas/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "cli",
    "cpp11",
    "data.table",
    "farver",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggrepel",
    "glue",
    "gridExtra",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lifecycle",
    "patchwork",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "ggwas.Rmd",
      "filename": "ggwas.html",
      "title": "ggwas: Modern GWAS Visualizations",
      "author": "Bartosz Czech",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting started",
        "Installation",
        "Reading data",
        "Core plots",
        "Manhattan plot",
        "Broken y-axis for extreme p-values",
        "Significance thresholds",
        "Effect-size confidence bound",
        "Palette and theme variations",
        "QQ plot",
        "Miami plot",
        "Locus zoom",
        "Novel visualizations",
        "Genome-wide p-value heatmap",
        "Effect-size volcano",
        "Circular Manhattan",
        "Summary dashboard",
        "Gene annotation and top hits",
        "Gene labels on peaks",
        "Top hits table",
        "Region highlights",
        "Genomic tracks",
        "Non-human organisms",
        "Multi-study comparisons",
        "Multi-trait Manhattan",
        "Enrichment Manhattan",
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