{
  "_id": "6a50b16a89c83ec243a2fb18",
  "Package": "ontologyPlot",
  "Type": "Package",
  "Title": "Visualising Sets of Ontological Terms",
  "Version": "1.7",
  "Date": "2024-02-20",
  "Encoding": "UTF-8",
  "Author": "Daniel Greene <dg333@cam.ac.uk>",
  "Maintainer": "Daniel Greene <dg333@cam.ac.uk>",
  "Description": "Create R plots visualising ontological terms and the\nrelationships between them with various graphical options -\nGreene et al. 2017 <doi:10.1093/bioinformatics/btw763>.",
  "License": "GPL (>= 2)",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-10 08:43:13 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://daniel-jg.r-universe.dev",
  "Date/Publication": "2024-02-21 02:32:41 UTC",
  "RemoteUrl": "https://github.com/cran/ontologyPlot",
  "RemoteRef": "HEAD",
  "RemoteSha": "c0744042dbb28811643d78fd816d77bde39ed539",
  "_user": "daniel-jg",
  "_type": "src",
  "_file": "ontologyPlot_1.7.tar.gz",
  "_fileid": "https://r2.ropensci.org/d26b0c47575e69340464f6ad6a733252ad669689e2016ba9d34b5f46d1282b0c",
  "_filesize": 1007627,
  "_sha256": "d26b0c47575e69340464f6ad6a733252ad669689e2016ba9d34b5f46d1282b0c",
  "_expires": "2026-10-18T08:46:32.000Z",
  "_created": "2026-07-10T08:43:13.000Z",
  "_published": "2026-07-10T08:46:34.073Z",
  "_jobs": [
    {
      "job": 86322592186,
      "time": 159,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8222671913"
    },
    {
      "job": 86322592150,
      "time": 125,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8222660190"
    },
    {
      "job": 86322592105,
      "time": 74,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8222642568"
    },
    {
      "job": 86322592113,
      "time": 107,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8222653951"
    },
    {
      "job": 86321959687,
      "time": 217,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8222613025"
    },
    {
      "job": 86322592098,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8222655411"
    },
    {
      "job": 86322592147,
      "time": 93,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8222649744"
    },
    {
      "job": 86322592114,
      "time": 88,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8222647368"
    },
    {
      "job": 86322592099,
      "time": 82,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8222645096"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055",
  "_status": "success",
  "_upstream": "https://github.com/cran/ontologyPlot",
  "_commit": {
    "id": "c0744042dbb28811643d78fd816d77bde39ed539",
    "author": "Daniel Greene <dg333@cam.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.7\n",
    "time": 1708482761
  },
  "_maintainer": {
    "name": "Daniel Greene",
    "email": "dg333@cam.ac.uk",
    "login": "daniel-jg",
    "description": "",
    "uuid": 25660818
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ontologyIndex",
      "role": "Imports"
    },
    {
      "package": "paintmap",
      "role": "Imports"
    },
    {
      "package": "Rgraphviz",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 7,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "daniel-jg",
      "count": 5,
      "uuid": 25660818
    }
  ],
  "_userbio": {
    "uuid": 25660818,
    "type": "user",
    "name": "Daniel",
    "followers": 4
  },
  "_downloads": {
    "count": 571,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ontologyPlot"
  },
  "_mentions": 2,
  "_searchresults": 66,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ontologyPlot.html",
    "manual.pdf"
  ],
  "_realowner": "daniel-jg",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2016-01-11"
    },
    {
      "version": "1.3",
      "date": "2016-09-09"
    },
    {
      "version": "1.4",
      "date": "2016-10-27"
    },
    {
      "version": "1.6",
      "date": "2021-02-10"
    },
    {
      "version": "1.7",
      "date": "2024-02-20"
    }
  ],
  "_exports": [
    "annotation_grid",
    "calibrate_sizes",
    "colour_by_frequency",
    "colour_by_population_frequency",
    "colour_by_term_set",
    "dot_string",
    "get_adjacency_matrix",
    "get_node_friendly_long_names",
    "get_pseudo_adjacency_matrix",
    "get_shortened_names",
    "grid_terms",
    "label_by_frequency",
    "label_by_term_set",
    "long_labels",
    "n_most_frequent_terms",
    "official_labels",
    "onto_plot",
    "p_values_for_occurrence_of_term_in_group",
    "plot_annotation_grid",
    "remove_links",
    "remove_terms_with_less_than_n_occurrences",
    "remove_uninformative_terms",
    "simple_cap",
    "simple_labels",
    "width_by_frequency",
    "width_by_significance",
    "write_dot"
  ],
  "_help": [
    {
      "page": "annotation_grid",
      "title": "Get logical matrix of term annotation for group of cases",
      "topics": [
        "annotation_grid"
      ]
    },
    {
      "page": "calibrate_sizes",
      "title": "Function to scale values between two given limits",
      "topics": [
        "calibrate_sizes"
      ]
    },
    {
      "page": "colour_by_frequency",
      "title": "Function to assign colours to terms based on frequency with which terms appear in 'term_sets'",
      "topics": [
        "colour_by_frequency"
      ]
    },
    {
      "page": "colour_by_population_frequency",
      "title": "Function to assign colours to terms based on population frequency of terms",
      "topics": [
        "colour_by_population_frequency"
      ]
    },
    {
      "page": "colour_by_term_set",
      "title": "Function to set colours of nodes in plot to distinguish terms belonging to different term sets",
      "topics": [
        "colour_by_term_set"
      ]
    },
    {
      "page": "dot_string",
      "title": "'ontology_plot' object to dot string",
      "topics": [
        "dot_string"
      ]
    },
    {
      "page": "get_adjacency_matrix",
      "title": "Get an adjacency matrix for a set of ontological terms",
      "topics": [
        "get_adjacency_matrix"
      ]
    },
    {
      "page": "get_node_friendly_long_names",
      "title": "Split up node labels across lines so they fit in nodes better",
      "topics": [
        "get_node_friendly_long_names"
      ]
    },
    {
      "page": "get_ontology_plot",
      "title": "Get 'ontology_plot' object",
      "topics": [
        "get_ontology_plot"
      ]
    },
    {
      "page": "get_pseudo_adjacency_matrix",
      "title": "Get an adjacency matrix for a set of ontological terms",
      "topics": [
        "get_pseudo_adjacency_matrix"
      ]
    },
    {
      "page": "get_shortened_names",
      "title": "Get human readable, shortened (where possible) ontological term names",
      "topics": [
        "get_shortened_names"
      ]
    },
    {
      "page": "grid_terms",
      "title": "Get set of HPO terms appropriate for showing in a grid",
      "topics": [
        "grid_terms"
      ]
    },
    {
      "page": "label_by_frequency",
      "title": "Function to get plot labels for terms based on frequency in 'term_sets'",
      "topics": [
        "label_by_frequency"
      ]
    },
    {
      "page": "label_by_term_set",
      "title": "Function to label nodes by 'term_set'",
      "topics": [
        "label_by_term_set"
      ]
    },
    {
      "page": "long_labels",
      "title": "Function to assign detailed node labels to terms",
      "topics": [
        "long_labels"
      ]
    },
    {
      "page": "n_most_frequent_terms",
      "title": "Select 'n' most prevalent terms in 'term_sets'",
      "topics": [
        "n_most_frequent_terms"
      ]
    },
    {
      "page": "official_labels",
      "title": "Get official names for terms",
      "topics": [
        "official_labels"
      ]
    },
    {
      "page": "onto_plot",
      "title": "Get 'ontology_plot' object",
      "topics": [
        "onto_plot"
      ]
    },
    {
      "page": "ontologyPlot-package",
      "title": "Functions for Visualising Sets of Ontological Terms",
      "topics": [
        "ontologyPlot-package",
        "ontologyPlot"
      ]
    },
    {
      "page": "p_values_for_occurrence_of_term_in_group",
      "title": "Get p-values for observing at least as many of each term as occur in 'term_sets' given the population frequencies of the terms",
      "topics": [
        "p_values_for_occurrence_of_term_in_group"
      ]
    },
    {
      "page": "plot_annotation_grid",
      "title": "Plot a logical matrix of term annotation",
      "topics": [
        "plot_annotation_grid"
      ]
    },
    {
      "page": "plot.ontology_plot",
      "title": "Plotting function for 'ontology_plot' object",
      "topics": [
        "plot.ontology_plot"
      ]
    },
    {
      "page": "print.ontology_plot",
      "title": "Print function for 'ontology_plot' object",
      "topics": [
        "print.ontology_plot"
      ]
    },
    {
      "page": "remove_links",
      "title": "Remove terms which just link two other terms together in a subontology",
      "topics": [
        "remove_links"
      ]
    },
    {
      "page": "remove_terms_with_less_than_n_occurrences",
      "title": "Remove terms with less than certain number of occurrences",
      "topics": [
        "remove_terms_with_less_than_n_occurrences"
      ]
    },
    {
      "page": "remove_uninformative_terms",
      "title": "Remove uninformative terms from union of all terms in set of annotations",
      "topics": [
        "remove_uninformative_terms"
      ]
    },
    {
      "page": "simple_cap",
      "title": "Capitalise words in character vector",
      "topics": [
        "simple_cap"
      ]
    },
    {
      "page": "simple_labels",
      "title": "Get simplified labels for terms",
      "topics": [
        "simple_labels"
      ]
    },
    {
      "page": "to_svg_string",
      "title": "Convert 'ontology_plot' to SVG string",
      "topics": [
        "to_svg_string"
      ]
    },
    {
      "page": "width_by_frequency",
      "title": "Function to get node sizes for terms based on frequency in 'term_sets'",
      "topics": [
        "width_by_frequency"
      ]
    },
    {
      "page": "width_by_significance",
      "title": "Function to get node sizes for terms based on statistical significance of seeing at least this number of each term in 'term_sets'",
      "topics": [
        "width_by_significance"
      ]
    },
    {
      "page": "write_dot",
      "title": "Export 'ontology_plot' object as dot file",
      "topics": [
        "write_dot"
      ]
    }
  ],
  "_rundeps": [
    "BiocGenerics",
    "generics",
    "graph",
    "ontologyIndex",
    "paintmap",
    "Rgraphviz"
  ],
  "_vignettes": [
    {
      "source": "plotting-ontological-terms.Rmd",
      "filename": "plotting-ontological-terms.html",
      "title": "Plotting Ontological Terms",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Plotting Terms",
        "Graphical parameters",
        "Frequencies",
        "Term sets",
        "Edge attributes",
        "Plots for publications"
      ],
      "created": "2016-09-09 18:09:18",
      "modified": "2024-02-21 02:32:41",
      "commits": 4
    },
    {
      "source": "plotting-term-grids.Rmd",
      "filename": "plotting-term-grids.html",
      "title": "Plotting Term Grids",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2016-09-09 18:09:18",
      "modified": "2024-02-21 02:32:41",
      "commits": 3
    }
  ],
  "_score": 4.743823221603751,
  "_indexed": true,
  "_nocasepkg": "ontologyplot",
  "_universes": [
    "daniel-jg"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7",
      "date": "2026-07-10T08:45:51.000Z",
      "distro": "resolute",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/b9b2c690e04bde2053a6f11882f1a7fc134ea866b3208d1d3468396a20b09db3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.7",
      "date": "2026-07-10T08:45:18.000Z",
      "distro": "resolute",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/b0c3a4efdc4b7b8a636da330639ef69683f48aed5b86c2766ce771095d16a4d9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7",
      "date": "2026-07-10T08:44:33.000Z",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/44bed3b15633742964dd462e57b01a9522597ff46678348f966069601820bcc3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.7",
      "date": "2026-07-10T08:45:00.000Z",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/b6ff5441c1623a3d87e8ffd2a6d1880af91a8279dc01fa4717d182019ad0dbac",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7",
      "date": "2026-07-10T08:45:23.000Z",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/5bd4eeab033aae926bfe381ef6808999c833cc503baa332cb68167cba8fd8776",
      "status": "success",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7",
      "date": "2026-07-10T08:44:41.000Z",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/38afb7eddb067035bddc7875e05817c4355d23e233dac8e64543791299f78255",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.7",
      "date": "2026-07-10T08:44:34.000Z",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/f02a1a5be12bce7f2363e58b34c5e05068617a39ebfbbdae27576fc4ce0d0dfb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.7",
      "date": "2026-07-10T08:44:28.000Z",
      "commit": "c0744042dbb28811643d78fd816d77bde39ed539",
      "fileid": "https://r2.ropensci.org/4e4298b7a389e029863983feb8be01f374b9841314e989ca4a92e8fbd461d274",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29080478055"
    }
  ]
}