{
  "_id": "6a4966a73c3572b93bf7f244",
  "Package": "gggenomes",
  "Title": "A Grammar of Graphics for Comparative Genomics",
  "Version": "1.1.3",
  "Authors@R": "c(\nperson(\"Thomas\", \"Hackl\", email = \"t.hackl@rug.nl\", role = c(\"aut\", \"cre\")),\nperson(\"Markus J.\", \"Ankenbrand\", email = \"iimog@iimog.org\", role = c(\"aut\")),\nperson(\"Bart\", \"van Adrichem\", role = c(\"aut\")),\nperson(\"Kristina\", \"Haslinger\", email = \"k.haslinger@rug.nl\", role = c(\"ctb\", \"sad\")))",
  "Description": "An extension of 'ggplot2' for creating complex genomic\nmaps. It builds on the power of 'ggplot2' and 'tidyverse'\nadding new 'ggplot2'-style geoms & positions and 'dplyr'-style\nverbs to manipulate the underlying data. It implements a layout\nconcept inspired by 'ggraph' and introduces tracks to bring\ntidiness to the mess that is genomics data.",
  "License": "MIT + file LICENSE",
  "URL": "https://thackl.github.io/gggenomes/,\nhttps://github.com/thackl/gggenomes",
  "BugReports": "https://github.com/thackl/gggenomes/issues",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libicu-dev libx11-dev",
  "Repository": "https://thackl.r-universe.dev",
  "Date/Publication": "2026-02-23 09:48:37 UTC",
  "RemoteUrl": "https://github.com/thackl/gggenomes",
  "RemoteRef": "HEAD",
  "RemoteSha": "0cdd5e759f53e4d27275a77541df51466d4f2918",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-23 07:27:35 UTC",
    "User": "root"
  },
  "Author": "Thomas Hackl [aut, cre],\nMarkus J. Ankenbrand [aut],\nBart van Adrichem [aut],\nKristina Haslinger [ctb, sad]",
  "Maintainer": "Thomas Hackl <t.hackl@rug.nl>",
  "_user": "thackl",
  "_type": "src",
  "_file": "gggenomes_1.1.3.tar.gz",
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  "_created": "2026-06-23T07:27:35.000Z",
  "_published": "2026-07-04T20:01:43.575Z",
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  "_buildurl": "https://github.com/r-universe/thackl/actions/runs/28009482707",
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  "_upstream": "https://github.com/thackl/gggenomes",
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    "description": "Assistant Professor for Eco-Evolutionary Bioinformatics",
    "uuid": 9363087
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  "_dependencies": [
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      "package": "R",
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      "package": "ggplot2",
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      "package": "vctrs",
      "role": "Imports"
    },
    {
      "package": "rlang",
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    },
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      "package": "dplyr",
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    },
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      "package": "tidyr",
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  ],
  "_topics": [
    "biological-data",
    "comparative-genomics",
    "genomics-visualization",
    "ggplot-extension",
    "ggplot2"
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  "_stars": 768,
  "_contributors": [
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    "description": "Assistant Professor for Eco-Evolutionary Bioinformatics"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gggenomes.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/thackl/gggenomes",
  "_realowner": "thackl",
  "_cranurl": true,
  "_releases": [
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      "version": "1.0.0",
      "date": "2024-06-28"
    },
    {
      "version": "1.0.1",
      "date": "2024-08-30"
    },
    {
      "version": "1.1.2",
      "date": "2025-11-14"
    },
    {
      "version": "1.1.3",
      "date": "2026-02-23"
    }
  ],
  "_exports": [
    "%<>%",
    "%>%",
    "add_class",
    "add_clusters",
    "add_feats",
    "add_links",
    "add_seqs",
    "add_subfeats",
    "add_sublinks",
    "align",
    "as_feats",
    "as_links",
    "as_seqs",
    "as_subfeats",
    "as_sublinks",
    "bins",
    "check_strand",
    "combine_strands",
    "def_formats",
    "def_names",
    "def_types",
    "drop_feat_layout",
    "drop_layout",
    "drop_link_layout",
    "drop_seq_layout",
    "ex",
    "feats",
    "feats0",
    "flip",
    "flip_seqs",
    "flip_strand",
    "focus",
    "genes",
    "geom_bin_label",
    "geom_coverage",
    "geom_feat",
    "geom_feat_label",
    "geom_feat_note",
    "geom_feat_tag",
    "geom_feat_text",
    "geom_gene",
    "geom_gene_label",
    "geom_gene_note",
    "geom_gene_tag",
    "geom_gene_text",
    "geom_link",
    "geom_link_curved",
    "geom_link_label",
    "geom_link_line",
    "geom_seq",
    "geom_seq_break",
    "geom_seq_label",
    "geom_variant",
    "geom_wiggle",
    "GeomFeatText",
    "get_seqs",
    "gggenomes",
    "has_vars",
    "if_reverse",
    "in_range",
    "introduce",
    "is_reverse",
    "label_bp",
    "layout",
    "layout_genomes",
    "layout_seqs",
    "links",
    "locate",
    "pick",
    "pick_by_tree",
    "pick_seqs",
    "pick_seqs_within",
    "position_pile",
    "position_sixframe",
    "position_strand",
    "position_strandpile",
    "position_variant",
    "PositionPile",
    "PositionSixframe",
    "PositionStrand",
    "PositionStrandpile",
    "pull_bins",
    "pull_feats",
    "pull_genes",
    "pull_links",
    "pull_seqs",
    "pull_track",
    "qc",
    "qw",
    "read_alitv",
    "read_bed",
    "read_blast",
    "read_context",
    "read_fai",
    "read_feats",
    "read_gbk",
    "read_gff3",
    "read_links",
    "read_paf",
    "read_seq_len",
    "read_seqs",
    "read_subfeats",
    "read_sublinks",
    "read_vcf",
    "require_vars",
    "scale_color_variant",
    "scale_shape_variant",
    "scale_x_bp",
    "seqs",
    "set_class",
    "set_seqs",
    "shift",
    "split_by",
    "strand_chr",
    "strand_int",
    "strand_lgl",
    "strip_class",
    "swap_if",
    "swap_query",
    "sync",
    "theme_gggenomes_clean",
    "track",
    "track_ids",
    "track_info",
    "unnest_exons",
    "vars_track",
    "width",
    "width0",
    "write_gff3"
  ],
  "_datasets": [
    {
      "name": "emale_ava",
      "title": "All-versus-all whole genome alignments of 6 EMALE genomes",
      "object": "emale_ava",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "file_id",
        "seq_id",
        "length",
        "start",
        "end",
        "strand",
        "seq_id2",
        "length2",
        "start2",
        "end2",
        "map_match",
        "map_length",
        "map_quality",
        "NM",
        "ms",
        "AS",
        "nn",
        "tp",
        "cm",
        "s1",
        "de",
        "rl",
        "cg"
      ],
      "rows": 125,
      "table": true,
      "tojson": true
    },
    {
      "name": "emale_cogs",
      "title": "Clusters of orthologs of 6 EMALE proteomes",
      "object": "emale_cogs",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "cluster_id",
        "feat_id",
        "cluster_size"
      ],
      "rows": 48,
      "table": true,
      "tojson": true
    },
    {
      "name": "emale_gc",
      "title": "Relative GC-content along 6 EMALE genomes",
      "object": "emale_gc",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "file_id",
        "seq_id",
        "start",
        "end",
        "name",
        "score"
      ],
      "rows": 2856,
      "table": true,
      "tojson": true
    },
    {
      "name": "emale_genes",
      "title": "Gene annotations if 6 EMALE genomes (endogenous virophages)",
      "object": "emale_genes",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "file_id",
        "seq_id",
        "start",
        "end",
        "strand",
        "type",
        "feat_id",
        "introns",
        "parent_ids",
        "source",
        "score",
        "phase",
        "width",
        "gc_content",
        "name",
        "Note",
        "geom_id"
      ],
      "rows": 143,
      "table": false,
      "tojson": true
    },
    {
      "name": "emale_ngaros",
      "title": "Integrated Ngaro retrotransposons of 6 EMALE genomes",
      "object": "emale_ngaros",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "file_id",
        "seq_id",
        "start",
        "end",
        "strand",
        "type",
        "feat_id",
        "introns",
        "parent_ids",
        "source",
        "score",
        "phase",
        "name",
        "geom_id"
      ],
      "rows": 3,
      "table": false,
      "tojson": true
    },
    {
      "name": "emale_prot_ava",
      "title": "All-versus-all alignments 6 EMALE proteomes",
      "object": "emale_prot_ava",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "file_id",
        "feat_id",
        "feat_id2",
        "pident",
        "length",
        "mismatch",
        "gapopen",
        "start",
        "end",
        "start2",
        "end2",
        "evalue",
        "bitscore"
      ],
      "rows": 827,
      "table": true,
      "tojson": true
    },
    {
      "name": "emale_seqs",
      "title": "Sequence index of 6 EMALE genomes (endogenous virophages)",
      "object": "emale_seqs",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "file_id",
        "seq_id",
        "seq_desc",
        "length"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    },
    {
      "name": "emale_tirs",
      "title": "Terminal inverted repeats of 6 EMALE genomes",
      "object": "emale_tirs",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "file_id",
        "seq_id",
        "start",
        "end",
        "strand",
        "type",
        "feat_id",
        "introns",
        "parent_ids",
        "source",
        "score",
        "phase",
        "name",
        "width",
        "geom_id"
      ],
      "rows": 12,
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_tracks",
      "title": "Add different types of tracks",
      "topics": [
        "add_clusters",
        "add_feats",
        "add_links",
        "add_subfeats",
        "add_sublinks",
        "add_tracks"
      ]
    },
    {
      "page": "add_seqs",
      "title": "Add seqs",
      "topics": [
        "add_seqs"
      ]
    },
    {
      "page": "align",
      "title": "Align genomes relative to target genes, feats, seqs, etc.",
      "topics": [
        "align"
      ]
    },
    {
      "page": "check_strand",
      "title": "Check strand",
      "topics": [
        "check_strand"
      ]
    },
    {
      "page": "combine_strands",
      "title": "Combine strands",
      "topics": [
        "combine_strands"
      ]
    },
    {
      "page": "def_formats",
      "title": "Defined file formats and extensions",
      "topics": [
        "def_formats"
      ]
    },
    {
      "page": "def_names",
      "title": "Default column names and types for defined formats",
      "topics": [
        "def_names",
        "def_types"
      ]
    },
    {
      "page": "drop_feat_layout",
      "title": "Drop feature layout",
      "topics": [
        "drop_feat_layout"
      ]
    },
    {
      "page": "drop_layout",
      "title": "Drop a genome layout",
      "topics": [
        "drop_layout"
      ]
    },
    {
      "page": "drop_link_layout",
      "title": "Drop a link layout",
      "topics": [
        "drop_link_layout"
      ]
    },
    {
      "page": "drop_seq_layout",
      "title": "Drop a seq layout",
      "topics": [
        "drop_seq_layout"
      ]
    },
    {
      "page": "emale_ava",
      "title": "All-versus-all whole genome alignments of 6 EMALE genomes",
      "topics": [
        "emale_ava"
      ]
    },
    {
      "page": "emale_cogs",
      "title": "Clusters of orthologs of 6 EMALE proteomes",
      "topics": [
        "emale_cogs"
      ]
    },
    {
      "page": "emale_gc",
      "title": "Relative GC-content along 6 EMALE genomes",
      "topics": [
        "emale_gc"
      ]
    },
    {
      "page": "emale_genes",
      "title": "Gene annotations if 6 EMALE genomes (endogenous virophages)",
      "topics": [
        "emale_genes"
      ]
    },
    {
      "page": "emale_ngaros",
      "title": "Integrated Ngaro retrotransposons of 6 EMALE genomes",
      "topics": [
        "emale_ngaros"
      ]
    },
    {
      "page": "emale_prot_ava",
      "title": "All-versus-all alignments 6 EMALE proteomes",
      "topics": [
        "emale_prot_ava"
      ]
    },
    {
      "page": "emale_seqs",
      "title": "Sequence index of 6 EMALE genomes (endogenous virophages)",
      "topics": [
        "emale_seqs"
      ]
    },
    {
      "page": "emale_tirs",
      "title": "Terminal inverted repeats of 6 EMALE genomes",
      "topics": [
        "emale_tirs"
      ]
    },
    {
      "page": "ex",
      "title": "Get path to gggenomes example files",
      "topics": [
        "ex"
      ]
    },
    {
      "page": "pull_track",
      "title": "Use tracks inside and outside geom_* calls",
      "topics": [
        "bins",
        "feats",
        "feats0",
        "genes",
        "links",
        "pull_bins",
        "pull_bins.gggenomes_layout",
        "pull_feats",
        "pull_genes",
        "pull_links",
        "pull_seqs",
        "pull_track",
        "seqs",
        "track"
      ]
    },
    {
      "page": "flip",
      "title": "Flip bins and sequences",
      "topics": [
        "flip",
        "flip_seqs",
        "sync"
      ]
    },
    {
      "page": "flip_strand",
      "title": "Flip strand",
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