{ "_id": "6a104337acfb0bcc41c9de54", "Package": "ontologyPlot", "Type": "Package", "Title": "Visualising Sets of Ontological Terms", "Version": "1.7", "Date": "2024-02-20", "Encoding": "UTF-8", "Author": "Daniel Greene ", "Maintainer": "Daniel Greene ", "Description": "Create R plots visualising ontological terms and the\nrelationships between them with various graphical options -\nGreene et al. 2017 .", "License": "GPL (>= 2)", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 07:01:06 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", "MD5sum": "7597ccf957b666bf6cb29201e5584c45", "_user": "daniel-jg", "_type": "src", "_file": "ontologyPlot_1.7.tar.gz", "_fileid": "c2cbbab0804c98aed0dff686ca5877866edd10c844778fbb705904ad6b46d089", "_filesize": 1008986, "_sha256": "c2cbbab0804c98aed0dff686ca5877866edd10c844778fbb705904ad6b46d089", "_created": "2026-05-11T07:01:06.000Z", "_published": "2026-05-22T11:51:19.703Z", "_distro": "noble", "_jobs": [ { "job": 77373820442, "time": 127, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6912180386" }, { "job": 77373820100, "time": 147, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6912183817" }, { "job": 77373820186, "time": 108, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6912173185" }, { "job": 77373820056, "time": 135, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6912180344" }, { "job": 77373819764, "time": 223, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6912143776" }, { "job": 77373819651, "time": 103, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159797682" }, { "job": 77373820405, "time": 75, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6912164283" }, { "job": 77373820078, "time": 78, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6912165121" }, { "job": 77373819991, "time": 76, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6912164633" } ], "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/ontologyPlot", "_commit": { "id": "c0744042dbb28811643d78fd816d77bde39ed539", "author": "Daniel Greene ", "committer": "cran-robot ", "message": "version 1.7\n", "time": 1708482761 }, "_maintainer": { "name": "Daniel Greene", "email": "dg333@cam.ac.uk", "login": "daniel-jg", "uuid": 25660818 }, "_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" }, "_downloads": { "count": 463, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ontologyPlot" }, "_mentions": 2, "_searchresults": 51, "_rbuild": "4.6.0", "_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": 4.631849462159819, "_indexed": true, "_nocasepkg": "ontologyplot", "_universes": [ "daniel-jg" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7", "date": "2026-05-11T07:03:18.000Z", "distro": "noble", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "a60490b5cb658259aa98e81ed3bc61c73b5e033d467fe834476a83d3eb170949", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" }, { "r": "4.6.0", "os": "linux", "version": "1.7", "date": "2026-05-11T07:03:31.000Z", "distro": "noble", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "d430a418b901cb93da30f199eae1e71218aea02d7b8abdbabead833c970f24c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" }, { "r": "4.5.3", "os": "mac", "version": "1.7", "date": "2026-05-11T07:02:55.000Z", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "ecb31b1c6c998bc5ddda56f5f2e69b998d237c90aaf5aace05f6a5c233280830", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" }, { "r": "4.6.0", "os": "mac", "version": "1.7", "date": "2026-05-11T07:03:13.000Z", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "03a3885223776dcc8774dc2f4c4c403727c2fcf96b99345fa739cd447623091a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" }, { "r": "4.7.0", "os": "win", "version": "1.7", "date": "2026-05-11T07:02:17.000Z", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "cd6496beebbb14690fbe631d15761f3f6282107b96ec82ed9b1d16560d87b2b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" }, { "r": "4.5.3", "os": "win", "version": "1.7", "date": "2026-05-11T07:02:19.000Z", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "e7dc71d3b4058680a5adc8c6c61f2936c6a19ebef9e9bba4690de6a319cb7312", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" }, { "r": "4.6.0", "os": "win", "version": "1.7", "date": "2026-05-11T07:02:17.000Z", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "8f2ffbf2bcc32c23064a0209247b29aaac0f7e5493b572fc558f781761f3525d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" }, { "r": "4.6.0", "os": "wasm", "version": "1.7", "date": "2026-05-22T11:51:01.000Z", "commit": "c0744042dbb28811643d78fd816d77bde39ed539", "fileid": "e29dfd96d47d17775d7e4c12c43ceaa47eaa73da615c7b0dba67adcdbe71f2d2", "status": "success", "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/25655156518" } ] }