{ "_id": "6a4941d618cdde069385e272", "Package": "ggtreeExtra", "Type": "Package", "Title": "An R Package To Add Geometric Layers On Circular Or Other Layout\nTree Of \"ggtree\"", "Version": "1.23.1", "Authors@R": "c(\nperson(given = \"Shuangbin\", family = \"Xu\", role = c(\"aut\", \"cre\"), email = \"xshuangbin@163.com\", comment = c(ORCID = \"0000-0003-3513-5362\")),\nperson(\"Guangchuang\", \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"ctb\"), comment = c(ORCID = \"0000-0002-6485-8781\"))\n)", "Description": "'ggtreeExtra' extends the method for mapping and\nvisualizing associated data on phylogenetic tree using\n'ggtree'. These associated data can be presented on the\nexternal panels to circular layout, fan layout, or other\nrectangular layout tree built by 'ggtree' with the grammar of\n'ggplot2'.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "URL": "https://github.com/YuLab-SMU/ggtreeExtra/", "BugReports": "https://github.com/YuLab-SMU/ggtreeExtra/issues", "ByteCompile": "true", "Roxygen": "list(markdown = TRUE)", "biocViews": "Software, Visualization, Phylogenetics, Annotation", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev make libicu-dev libpng-dev libuv1-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-06-04 06:26:22 UTC", "RemoteUrl": "https://github.com/bioc/ggtreeExtra", "RemoteRef": "HEAD", "RemoteSha": "b353b67109d84f344f63b5607567357a5c1a58e2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 08:56:12 UTC", "User": "root" }, "Author": "Shuangbin Xu [aut, cre] (ORCID:\n),\nGuangchuang Yu [aut, ctb] (ORCID:\n)", "Maintainer": "Shuangbin Xu ", "_user": "bioc", "_type": "src", "_file": "ggtreeExtra_1.23.1.tar.gz", "_fileid": "https://r2.ropensci.org/a6faff16d7570c807d1b51d3169ecf3e3ecafb6cab3ba11d62747b7acc78cf18", "_filesize": 1269810, "_sha256": "a6faff16d7570c807d1b51d3169ecf3e3ecafb6cab3ba11d62747b7acc78cf18", "_expires": "2026-10-12T17:24:36.000Z", "_created": "2026-07-04T08:56:12.000Z", "_published": "2026-07-04T17:24:38.391Z", "_bioccheck": { "error": 1, "warning": 2, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307", "_status": "success", "_upstream": "https://github.com/bioc/ggtreeExtra", "_commit": { "id": "b353b67109d84f344f63b5607567357a5c1a58e2", "author": "xiangpin ", "committer": "xiangpin ", "message": "update news and bump version\n", "time": 1780554382 }, "_maintainer": { "name": "Shuangbin Xu", "email": "xshuangbin@163.com", "login": "xiangpin", "description": "", "uuid": 17870644, "orcid": "0000-0003-3513-5362" }, "_distro": "resolute", "_jobs": [ { "job": 85151969157, "time": 161, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8080248438" }, { "job": 85151969134, "time": 229, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8080256586" }, { "job": 85151969233, "time": 165, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8080248978" }, { "job": 85151969467, "time": 87, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8080466577" }, { "job": 85151969203, "time": 89, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8080485664" }, { "job": 85151968982, "time": 221, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8080227316" }, { "job": 85151969450, "time": 161, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8080248165" }, { "job": 85151969221, "time": 103, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8080241191" }, { "job": 85151969518, "time": 118, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8080243317" }, { "job": 85151969196, "time": 102, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8080241102" } ], "_registered": true, "_dependencies": [ { "package": "ggplot2", "version": ">= 4.0.0", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "ggnewscale", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggtree", "role": "Imports" }, { "package": "tidytree", "version": ">= 0.3.9", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "yulab.utils", "role": "Imports" }, { "package": "treeio", "role": "Suggests" }, { "package": "ggstar", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "prettydoc", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "pillar", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-27", "n": 2 }, { "week": "2025-33", "n": 1 }, { "week": "2025-38", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-45", "n": 1 }, { "week": "2026-02", "n": 3 }, { "week": "2026-04", "n": 1 }, { "week": "2026-18", "n": 3 }, { "week": "2026-23", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.1", "bioc": "3.24" }, { "branch": "release", "version": "1.22.1", "bioc": "3.23" } ], "_topics": [ "software", "visualization", "phylogenetics", "annotation" ], "_stars": 98, "_contributors": [ { "user": "xiangpin", "count": 295, "uuid": 17870644 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 8, "uuid": 2746443 }, { "user": "guangchuangyu", "count": 6, "uuid": 626539 }, { "user": "gaospecial", "count": 1, "uuid": 107597 }, { "user": "lshep", "count": 1, "uuid": 18724380 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 2, "_devurl": "https://github.com/yulab-smu/ggtreeextra", "_searchresults": 684, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ggtreeExtra.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yulab-smu/ggtreeextra", "_realowner": "bioc", "_cranurl": false, "_exports": [ "%>%", "fruit_plot", "geom_fruit", "geom_fruit_list", "ggplot_add", "position_dodgex", "position_dodgex2", "position_identityx", "position_jitterdodgex", "position_jitterx", "position_points_jitterx", "position_points_sinax", "position_raincloudx", "position_stackx", "PositionJitterdodgex", "PositionJitterx", "td_filter", "td_unnest" ], "_help": [ { "page": "geom_fruit", "title": "plot tree with associated data in another method.", "topics": [ "fruit_plot", "geom_fruit" ] }, { "page": "geom_fruit_list", "title": "geom_fruit_list", "topics": [ "geom_fruit_list" ] }, { "page": "position_dodgex", "title": "Dodge overlapping objects side-to-side which can be shifted verically or horizontally.", "concept": [ "position adjustments" ], "topics": [ "position_dodgex", "position_dodgex2" ] }, { "page": "position_identityx", "title": "adjust identity position which can be shifted vertically or horizontally.", "concept": [ "position adjustments" ], "topics": [ "position_identityx" ] }, { "page": "position_jitterdodgex", "title": "Simultaneously dodge and jitter, and the whole layer can be shifted vertically or horizontally", "topics": [ "position_jitterdodgex" ] }, { "page": "position_jitterx", "title": "Jitter points to avoid overplotting, and the whole points can be shifted vertically or horizontally", "topics": [ "position_jitterx" ] }, { "page": "position_points_jitterx", "title": "Randomly jitter the points in a ridgeline plot which can be shifted horizontally", "topics": [ "position_points_jitterx" ] }, { "page": "position_points_sinax", "title": "adjust ridgeline plot position which can be shifted vertically or horizontally.", "concept": [ "position adjustments" ], "topics": [ "position_points_sinax" ] }, { "page": "position_raincloudx", "title": "Create a cloud of randomly jittered points below a ridgeline plot which can be shifted horizontally", "topics": [ "position_raincloudx" ] }, { "page": "position_stackx", "title": "Stack overlapping objects which can be shifted vertically or horizontally", "topics": [ "position_stackx" ] }, { "page": "ggplot2-ggproto", "title": "PositionDodgex", "topics": [ "PositionDodgex", "PositionDodgex2", "PositionIdentityx", "PositionPointsJitterx", "PositionPointsSinax", "PositionRaincloudx", "PositionStackx" ] }, { "page": "PositionJitterdodgex", "title": "PositionJitterdodgex", "topics": [ "PositionJitterdodgex" ] }, { "page": "PositionJitterx", "title": "PositionJitterx", "topics": [ "PositionJitterx" ] } ], "_readme": "https://github.com/bioc/ggtreeExtra/raw/HEAD/README.md", "_rundeps": [ "ape", "aplot", "base64enc", "bslib", "cachem", "cli", "cpp11", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "ggfun", "ggiraph", "ggnewscale", "ggplot2", "ggplotify", "ggtree", "glue", "gridGraphics", "gtable", "highr", "htmltools", "htmlwidgets", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "memoise", "mime", "nlme", "patchwork", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "systemfonts", "tibble", "tidyr", "tidyselect", "tidytree", "tinytex", "treeio", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml", "yulab.utils" ], "_vignettes": [ { "source": "ggtreeExtra.Rmd", "filename": "ggtreeExtra.html", "title": "ggtreeExtra", "author": "| Shuangbin Xu and GuangChuang Yu | School of Basic Medical Sciences, Southern Medical University", "engine": "knitr::rmarkdown", "headings": [ "Setup", "1. Introduction", "2. Install", "3. Usage", "3.1 add single layer", "3.2 add multiple layers on the same position.", "4. Need helps?", "5. Session information", "6. Reference" ], "created": "2020-07-07 09:04:50", "modified": "2025-08-11 11:22:50", "commits": 19 } ], "_score": 10.2576459415716, "_indexed": true, "_nocasepkg": "ggtreeextra", "_universes": [ "bioc", "xiangpin", "yulab-smu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.1", "date": "2026-07-04T08:59:43.000Z", "distro": "resolute", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/0bee57a54a00663a8d57a7a7014b5bcb861904ff33f541311c8dd3ef8b5dfe77", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" }, { "r": "4.6.1", "os": "linux", "version": "1.23.1", "date": "2026-07-04T08:58:50.000Z", "distro": "resolute", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/96bcf5429757e4d057a945b7ee1505bae4793f00ae1e74cad66c7e8fcf500b51", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" }, { "r": "4.5.3", "os": "mac", "version": "1.23.1", "date": "2026-07-04T09:29:39.000Z", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/cb2dbb1b4330c39dbf7d0bf2e8b05efe2ec1a48a8e642494d1a3b63b7130fba1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" }, { "r": "4.6.1", "os": "mac", "version": "1.23.1", "date": "2026-07-04T09:32:13.000Z", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/383c5eb184db01870f35bd88a445a83f79f237670b8b633a8e359c52b33eef0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.1", "date": "2026-07-04T08:59:12.000Z", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/025a2d146993098d0232275f679d46000d4f821e1d0b5a363e014a6ffbe7ee8f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" }, { "r": "4.7.0", "os": "win", "version": "1.23.1", "date": "2026-07-04T08:57:31.000Z", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/a1ebef5c1821567164cc1f2687e97d338bbfc5f819ceb769fce6603d8fcc3904", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" }, { "r": "4.5.3", "os": "win", "version": "1.23.1", "date": "2026-07-04T08:57:45.000Z", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/a7f7efdbfa3eb6a481330137f3fc6e40a45f26bf264457cbf405d4442f9a4626", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" }, { "r": "4.6.1", "os": "win", "version": "1.23.1", "date": "2026-07-04T08:57:28.000Z", "commit": "b353b67109d84f344f63b5607567357a5c1a58e2", "fileid": "https://r2.ropensci.org/f6da21cf62d91e452228d79e0befa70edb6c585b136e8c0715b350760c827c69", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28701098307" } ] }