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  "Package": "locusviz",
  "Type": "Package",
  "Title": "Yet Another Locus Visualization Package in R",
  "Version": "0.3.0",
  "Author": "Masahiro Kanai",
  "Maintainer": "Masahiro Kanai <mkanai@broadinstitute.org>",
  "Description": "This package provides various functions to visualize GWAS\ndata for a locus of interest using ggplot2.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://mkanai.r-universe.dev",
  "Date/Publication": "2026-08-14 07:50:30 UTC",
  "RemoteUrl": "https://github.com/mkanai/locusviz",
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    "get_pfam_domains",
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    "jitter_labels",
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    "stat_summary_irq",
    "trans_loglog_p",
    "UpSet2",
    "variant_str",
    "variant_str2",
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        "tss"
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  "_help": [
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      "page": "annotate_r2",
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      ]
    },
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    {
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      "topics": [
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    },
    {
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        "geom_jitter_text"
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      "topics": [
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    },
    {
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      "title": "Get default ggplot2 theme for locusviz plots",
      "topics": [
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    },
    {
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      "topics": [
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    },
    {
      "page": "get_gnomad_colors",
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      "topics": [
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      ]
    },
    {
      "page": "get_pfam_domains",
      "title": "Get Pfam domain annotations for a gene",
      "topics": [
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      ]
    },
    {
      "page": "get_tss_gene_body",
      "title": "Extract TSS and gene body information from TxDb",
      "topics": [
        "get_tss_gene_body"
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    },
    {
      "page": "highlight_vline",
      "title": "Add vertical highlight lines to a plot",
      "topics": [
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      ]
    },
    {
      "page": "jitter_labels",
      "title": "Jitter labels to avoid horizontal overlap",
      "topics": [
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    },
    {
      "page": "liftover_variant",
      "title": "Liftover variant positions between genome builds",
      "topics": [
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    },
    {
      "page": "load_txdb",
      "title": "Load transcript database for gene annotations",
      "topics": [
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    },
    {
      "page": "mean_ci",
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      "topics": [
        "mean_ci"
      ]
    },
    {
      "page": "median_ci",
      "title": "Median confidence interval via bootstrap",
      "topics": [
        "median_ci"
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    },
    {
      "page": "na_and",
      "title": "NA-safe AND operation",
      "topics": [
        "na_and"
      ]
    },
    {
      "page": "na_or",
      "title": "NA-safe OR operation",
      "topics": [
        "na_or"
      ]
    },
    {
      "page": "normalize_rank",
      "title": "Normalize scores by rank with exponential decay",
      "topics": [
        "normalize_rank"
      ]
    },
    {
      "page": "or_else",
      "title": "Return first non-NA value",
      "topics": [
        "or_else"
      ]
    },
    {
      "page": "or_missing",
      "title": "Conditionally return value or NULL",
      "topics": [
        "or_missing"
      ]
    },
    {
      "page": "parse_variant",
      "title": "Parse variant string into components",
      "topics": [
        "parse_variant"
      ]
    },
    {
      "page": "plot_fm_panel",
      "title": "Create fine-mapping panel",
      "topics": [
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      ]
    },
    {
      "page": "plot_gene_panel",
      "title": "Create gene track panel",
      "topics": [
        "plot_gene_panel"
      ]
    },
    {
      "page": "plot_gene_score_panel",
      "title": "Create gene score visualization panel",
      "topics": [
        "plot_gene_score_panel"
      ]
    },
    {
      "page": "plot_locuszoom",
      "title": "Create LocusZoom-style visualization",
      "topics": [
        "plot_locuszoom"
      ]
    },
    {
      "page": "plot_lollipop",
      "title": "Create lollipop plot for variant effects",
      "topics": [
        "plot_lollipop"
      ]
    },
    {
      "page": "plot_manhattan_panel",
      "title": "Create Manhattan plot panel",
      "topics": [
        "plot_manhattan_panel"
      ]
    },
    {
      "page": "plot_r2_panel",
      "title": "Create r² (linkage disequilibrium) panel",
      "topics": [
        "plot_r2_panel"
      ]
    },
    {
      "page": "plot_upset",
      "title": "Create UpSet plot for set intersections",
      "topics": [
        "plot_upset"
      ]
    },
    {
      "page": "plot_upset_bar",
      "title": "Plot UpSet bar panel",
      "topics": [
        "plot_upset_bar"
      ]
    },
    {
      "page": "plot_upset_matrix",
      "title": "Plot UpSet matrix panel",
      "topics": [
        "plot_upset_matrix"
      ]
    },
    {
      "page": "preprocess",
      "title": "Preprocess GWAS data for visualization",
      "topics": [
        "preprocess"
      ]
    },
    {
      "page": "scale_color_chromosome",
      "title": "Create chromosome color scale for Manhattan plots",
      "topics": [
        "scale_color_chromosome"
      ]
    },
    {
      "page": "scale_x_chromosome",
      "title": "Create chromosome x-axis scale for genome-wide plots",
      "topics": [
        "scale_x_chromosome"
      ]
    },
    {
      "page": "spearman_ci",
      "title": "Spearman correlation confidence interval",
      "topics": [
        "spearman_ci"
      ]
    },
    {
      "page": "stat_summary_irq",
      "title": "Summary statistic with interquartile range",
      "topics": [
        "stat_summary_irq"
      ]
    },
    {
      "page": "trans_loglog_p",
      "title": "Create log-log transformation for p-values",
      "topics": [
        "trans_loglog_p"
      ]
    },
    {
      "page": "tss_v19_hg19",
      "title": "TSS and gene body data for GENCODE v19 (hg19/GRCh37)",
      "topics": [
        "tss_v19_hg19"
      ]
    },
    {
      "page": "tss_v34_hg38",
      "title": "TSS and gene body data for GENCODE v34 (hg38/GRCh38)",
      "topics": [
        "tss_v34_hg38"
      ]
    },
    {
      "page": "tss_v39_hg38",
      "title": "TSS and gene body data for GENCODE v39 (hg38/GRCh38)",
      "topics": [
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      ]
    },
    {
      "page": "UpSet2",
      "title": "Modified UpSet plot",
      "topics": [
        "UpSet2"
      ]
    },
    {
      "page": "variant_str",
      "title": "Create variant string from components",
      "topics": [
        "variant_str"
      ]
    },
    {
      "page": "variant_str2",
      "title": "Create variant string from locus and alleles",
      "topics": [
        "variant_str2"
      ]
    },
    {
      "page": "write_txdb_files",
      "title": "Write TxDb and TSS data files",
      "topics": [
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      ]
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  ],
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