{ "_id": "6a1af0361d7bb097a09f67c8", "Package": "tanggle", "Type": "Package", "Title": "Visualization of Phylogenetic Networks", "Version": "1.19.0", "Authors@R": "c(person(\"Klaus\", \"Schliep\", email=\"klaus.schliep@gmail.com\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-2941-0161\")),\nperson(\"Marta\", \"Vidal-Garcia\", role=\"aut\"),\nperson(\"Claudia\", \"Solis-Lemus\", role=\"aut\",\nemail=\"solislemus@wisc.edu\", comment = c(ORCID = \"0000-0002-9789-8915\")),\nperson(\"Leann\", \"Biancani\", role=\"aut\"),\nperson(\"Eren\", \"Ada\", role=\"aut\"),\nperson(\"L. Francisco\", \"Henao Diaz\", role=\"aut\"),\nperson(\"Guangchuang\", \"Yu\", role = c(\"ctb\")),\nperson(\"Joshua\", \"Justison\", role=\"aut\"))", "Description": "Offers functions for plotting split (or implicit) networks\n(unrooted, undirected) and explicit networks (rooted, directed)\nwith reticulations extending. 'ggtree' and using functions from\n'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017]\nto allow the visualization of phylogenetic networks using the\n'ggplot2' syntax. It offers an alternative to the plot\nfunctions already available in 'ape' Paradis and Schliep (2019)\n and 'phangorn' Schliep\n(2011) .", "VignetteBuilder": "knitr", "biocViews": "Software, Visualization, Phylogenetics, Alignment,\nClustering, MultipleSequenceAlignment, DataImport", "License": "Artistic-2.0", "URL": "https://klausvigo.github.io/tanggle/,\nhttps://github.com/KlausVigo/tanggle", "BugReports": "https://github.com/KlausVigo/tanggle/issues", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Roxygen": "list(old_usage = TRUE)", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:49 UTC", "RemoteUrl": "https://github.com/bioc/tanggle", "RemoteRef": "HEAD", "RemoteSha": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:43:23 UTC", "User": "root" }, "Author": "Klaus Schliep [aut, cre] (ORCID:\n),\nMarta Vidal-Garcia [aut],\nClaudia Solis-Lemus [aut] (ORCID:\n),\nLeann Biancani [aut],\nEren Ada [aut],\nL. Francisco Henao Diaz [aut],\nGuangchuang Yu [ctb],\nJoshua Justison [aut]", "Maintainer": "Klaus Schliep ", "MD5sum": "0ffbfda4f6e20e99391ad35ef9fa2ba5", "_user": "bioc", "_type": "src", "_file": "tanggle_1.19.0.tar.gz", "_fileid": "54c05762d035569f5a7a6c9eb5090a259b44539c122230bdf1686a37f23b23ab", "_filesize": 1760904, "_sha256": "54c05762d035569f5a7a6c9eb5090a259b44539c122230bdf1686a37f23b23ab", "_created": "2026-05-30T09:43:23.000Z", "_published": "2026-05-30T14:12:06.562Z", "_jobs": [ { "job": 78640430818, "time": 242, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307431006" }, { "job": 78640430822, "time": 229, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307431253" }, { "job": 78640430825, "time": 188, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307425827" }, { "job": 78640430827, "time": 104, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308771663" }, { "job": 78640430830, "time": 93, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308769960" }, { "job": 78639773123, "time": 209, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307267157" }, { "job": 78640430823, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307421610" }, { "job": 78640430853, "time": 107, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307416310" }, { "job": 78640430832, "time": 105, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307416077" }, { "job": 78640430849, "time": 100, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307415639" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/tanggle", "_commit": { "id": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381009 }, "_maintainer": { "name": "Klaus Schliep", "email": "klaus.schliep@gmail.com", "login": "klausvigo", "description": "Senior Scientist at TU Graz", "uuid": 3372431, "orcid": "0000-0003-2941-0161" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "ggplot2", "version": ">= 3.0.0", "role": "Depends" }, { "package": "ggtree", "role": "Depends" }, { "package": "ape", "version": ">= 5.0", "role": "Imports" }, { "package": "phangorn", "version": ">= 2.12", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tinytest", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "ggimage", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 6 }, { "week": "2025-27", "n": 1 }, { "week": "2025-28", "n": 8 }, { "week": "2025-42", "n": 3 }, { "week": "2025-43", "n": 9 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "software", "visualization", "phylogenetics", "alignment", "clustering", "multiplesequencealignment", "dataimport", "phylogenetic-networks" ], "_stars": 11, "_contributors": [ { "user": "klausvigo", "count": 91, "uuid": 3372431 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "marta-vidalgarcia", "count": 7, "uuid": 18388042 }, { "user": "crsl4", "count": 5, "uuid": 8419800 }, { "user": "nturaga", "count": 4, "uuid": 2746443 }, { "user": "jjustison", "count": 3, "uuid": 19258474 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 329, "source": "https://www.bioconductor.org/packages/stats/bioc/tanggle" }, "_devurl": "https://github.com/klausvigo/tanggle", "_pkgdown": "https://klausvigo.github.io/tanggle/", "_searchresults": 90, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/tanggle.html", "manual.pdf" ], "_homeurl": "https://github.com/klausvigo/tanggle", "_realowner": "bioc", "_cranurl": false, "_exports": [ "geom_splitnet", "ggevonet", "ggsplitnet", "minimize_overlap", "node_depth_evonet", "swap_hybrid_minor" ], "_help": [ { "page": "geom_splitnet", "title": "geom_splitnet", "topics": [ "geom_splitnet" ] }, { "page": "ggevonet", "title": "ggevonet", "topics": [ "ggevonet" ] }, { "page": "ggsplitnet", "title": "ggsplitnet", "topics": [ "ggsplitnet" ] }, { "page": "minimize_overlap", "title": "minimize_overlap reduces reticulation lines crossing over in plots", "topics": [ "minimize_overlap" ] }, { "page": "node_depth_evonet", "title": "Depth of Nodes", "topics": [ "node_depth_evonet" ] }, { "page": "swap_hybrid_minor", "title": "swap_hybrid_minor", "topics": [ "swap_hybrid_minor" ] } ], "_pkglogo": "https://github.com/bioc/tanggle/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/tanggle/raw/HEAD/README.md", "_rundeps": [ "ape", "aplot", "base64enc", "bslib", "cachem", "cli", "cpp11", "digest", "dplyr", "evaluate", "farver", "fastmap", "fastmatch", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "ggfun", "ggiraph", "ggplot2", "ggplotify", "ggtree", "glue", "gridGraphics", "gtable", "highr", "htmltools", "htmlwidgets", "igraph", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mime", "nlme", "patchwork", "phangorn", "pillar", "pkgconfig", "purrr", "quadprog", "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": "tanggle_vignette_espanol.Rmd", "filename": "tanggle_vignette_espanol.html", "title": "tanggle: Visualización de redes filogenéticas con ggplot2", "author": "Klaus Schliep, Marta Vidal-García, Leann Biancani, Francisco Henao-Diaz, Eren Ada, Claudia Solís-Lemus", "engine": "knitr::rmarkdown", "headings": [ "Introducción", "Lista de funciones", "Para empezar", "Redes dividida o implicitas", "Tipos de datos", "Para graficar una Red Dividida", "Para graficar una Red Explícita", "Resumen", "Session info", "References" ], "created": "2022-01-13 15:11:49", "modified": "2025-07-11 14:15:01", "commits": 2 }, { "source": "tanggle_vignette.Rmd", "filename": "tanggle_vignette.html", "title": "tanggle: Visualization of phylogenetic networks in a ggplot2 framework", "author": "Klaus Schliep, Marta Vidal-García, Leann Biancani, Francisco Henao Diaz, Eren Ada, Claudia Solís-Lemus", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "List of functions", "Getting started", "Split Networks", "Data Types", "Plotting a Split Network:", "Plotting Explicit Networks", "Summary", "Session info", "References" ], "created": "2020-11-07 01:21:41", "modified": "2025-07-11 14:15:01", "commits": 10 } ], "_score": 7.539703238947825, "_indexed": true, "_nocasepkg": "tanggle", "_universes": [ "bioc", "klausvigo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T10:11:52.000Z", "distro": "noble", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "68173bf9a7158f5fccbb3153813164167034dccdfb4cadfc5dcb03129d661bf4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T10:10:57.000Z", "distro": "noble", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "ed8bfd61f09a090df812bd4ebce551549064be52d112c6d67680c20594da86c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-05-30T14:11:25.000Z", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "85fb7346b6f58ca532d8c751b51b89517fd33d9d14657192a67884f886038425", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-05-30T14:11:07.000Z", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "0c94a0ad47c37b757f61fb3930b74ebd2df839bf1f1a741ffaf5e8200c2dbf95", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-05-30T10:10:48.000Z", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "2f705b4924091505e2a7585bf76300eb67ebfdeca6da6bca745e583ded9f70e0", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-05-30T10:09:07.000Z", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "0c8028b65cd124c11b1d1e3a1cfce4e1be77c4d68f9294cc5c2953d934e16680", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-05-30T10:09:01.000Z", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "96a8a32f3bd7b31e4004c9cdbb1c801136da90acebbf2b2587a8fb52b55b26e7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" }, { "r": "4.6.0", "os": "win", "version": "1.19.0", "date": "2026-05-30T10:08:57.000Z", "commit": "106f9e7ffdc1b0c7284d6aad318915dc20f25318", "fileid": "b9782650f8ebe4e212b67654973b2cf91a660483a106b5860a023db54da057ca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676638265" } ] }