{
  "_id": "6a2152e0cd65a98ecbd2d94d",
  "Package": "clustree",
  "Type": "Package",
  "Title": "Visualise Clusterings at Different Resolutions",
  "Version": "0.5.1",
  "Date": "2023-11-05",
  "Authors@R": "c(person(\"Luke\", \"Zappia\", role = c(\"aut\", \"cre\"),\nemail = \"luke@lazappi.id.au\",\ncomment = c(ORCID = \"0000-0001-7744-8565\")),\nperson(\"Alicia\", \"Oshlack\", role = c(\"aut\"),\nemail = \"alicia.oshlack@petermac.org\",\ncomment = c(ORCID = \"0000-0001-9788-5690\")),\nperson(\"Andrea\", \"Rau\", role = c(\"ctb\"),\nemail = \"andrea.rau@inra.fr\"),\nperson(\"Paul\", \"Hoffman\", role = c(\"ctb\"),\nemail = \"phoffman@nygenome.org\",\ncomment = c(ORCID = \"0000-0002-7693-8957\")))",
  "Maintainer": "Luke Zappia <luke@lazappi.id.au>",
  "Description": "Deciding what resolution to use can be a difficult\nquestion when approaching a clustering analysis. One way to\napproach this problem is to look at how samples move as the\nnumber of clusters increases. This package allows you to\nproduce clustering trees, a visualisation for interrogating\nclusterings as resolution increases.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://github.com/lazappi/clustree,\nhttps://lazappi.github.io/clustree/",
  "BugReports": "https://github.com/lazappi/clustree/issues",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "Language": "en-GB",
  "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libxml2-dev",
  "Repository": "https://lazappi.r-universe.dev",
  "Date/Publication": "2023-11-08 09:24:34 UTC",
  "RemoteUrl": "https://github.com/lazappi/clustree",
  "RemoteRef": "HEAD",
  "RemoteSha": "24900bdf459c29812c716ba9f889c58685f957ed",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 10:21:23 UTC",
    "User": "root"
  },
  "Author": "Luke Zappia [aut, cre] (ORCID: <https://orcid.org/0000-0001-7744-8565>),\nAlicia Oshlack [aut] (ORCID: <https://orcid.org/0000-0001-9788-5690>),\nAndrea Rau [ctb],\nPaul Hoffman [ctb] (ORCID: <https://orcid.org/0000-0002-7693-8957>)",
  "MD5sum": "a2bce964b2bed62dac21208a36a4977c",
  "_user": "lazappi",
  "_type": "src",
  "_file": "clustree_0.5.1.tar.gz",
  "_fileid": "abe0fa6571f9c9937a83a9f64fd0279531b215c89ef47d6500c8162e12691e83",
  "_filesize": 2462571,
  "_sha256": "abe0fa6571f9c9937a83a9f64fd0279531b215c89ef47d6500c8162e12691e83",
  "_created": "2026-06-04T10:21:23.000Z",
  "_published": "2026-06-04T10:26:40.558Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79498512992,
      "time": 236,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7409047963"
    },
    {
      "job": 79498513042,
      "time": 200,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409035940"
    },
    {
      "job": 79498512929,
      "time": 130,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7409011698"
    },
    {
      "job": 79498512987,
      "time": 129,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409005331"
    },
    {
      "job": 79497708046,
      "time": 300,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7408965813"
    },
    {
      "job": 79498512927,
      "time": 167,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409024331"
    },
    {
      "job": 79498512982,
      "time": 274,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7409060985"
    },
    {
      "job": 79498512985,
      "time": 145,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7409016980"
    },
    {
      "job": 79498512964,
      "time": 149,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7409018379"
    }
  ],
  "_buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/lazappi/clustree",
  "_commit": {
    "id": "24900bdf459c29812c716ba9f889c58685f957ed",
    "author": "Luke Zappia <lazappi@users.noreply.github.com>",
    "committer": "Luke Zappia <lazappi@users.noreply.github.com>",
    "message": "Fix code coverage badge\n",
    "time": 1699435474
  },
  "_maintainer": {
    "name": "Luke Zappia",
    "email": "luke@lazappi.id.au",
    "login": "lazappi",
    "bluesky": "@lazappi.bsky.social",
    "linkedin": "in/lazappi",
    "orcid": "0000-0001-7744-8565",
    "description": "Bioinformatician, data scientist, developer",
    "uuid": 6869320
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "ggraph",
      "role": "Depends"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.4.0",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "tidygraph",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "version": ">= 2.3.0",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    }
  ],
  "_owner": "lazappi",
  "_selfowned": true,
  "_usedby": 5,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "clustering",
    "clustering-trees",
    "visualisation",
    "visualization"
  ],
  "_stars": 258,
  "_contributors": [
    {
      "user": "lazappi",
      "count": 279,
      "uuid": 6869320
    },
    {
      "user": "andreamrau",
      "count": 1,
      "uuid": 12795415
    },
    {
      "user": "mllg",
      "count": 1,
      "uuid": 1260920
    },
    {
      "user": "mojaveazure",
      "count": 1,
      "uuid": 11035068
    }
  ],
  "_userbio": {
    "uuid": 6869320,
    "type": "user",
    "name": "Luke Zappia",
    "description": "Bioinformatician, data scientist, developer"
  },
  "_downloads": {
    "count": 4652,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/clustree"
  },
  "_mentions": 8,
  "_devurl": "https://github.com/lazappi/clustree",
  "_pkgdown": "https://lazappi.github.io/clustree/",
  "_searchresults": 3248,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/clustree.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/lazappi/clustree",
  "_realowner": "lazappi",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.1",
      "date": "2018-03-28"
    },
    {
      "version": "0.1.2",
      "date": "2018-04-20"
    },
    {
      "version": "0.2.0",
      "date": "2018-06-24"
    },
    {
      "version": "0.2.1",
      "date": "2018-07-09"
    },
    {
      "version": "0.2.2",
      "date": "2018-07-10"
    },
    {
      "version": "0.3.0",
      "date": "2019-02-24"
    },
    {
      "version": "0.4.0",
      "date": "2019-04-18"
    },
    {
      "version": "0.4.1",
      "date": "2019-08-21"
    },
    {
      "version": "0.4.2",
      "date": "2020-01-29"
    },
    {
      "version": "0.4.3",
      "date": "2020-06-14"
    },
    {
      "version": "0.4.4",
      "date": "2021-11-08"
    },
    {
      "version": "0.5.0",
      "date": "2022-06-25"
    },
    {
      "version": "0.5.1",
      "date": "2023-11-05"
    }
  ],
  "_exports": [
    "clustree",
    "clustree_overlay"
  ],
  "_datasets": [
    {
      "name": "nba_clusts",
      "title": "Clustered NBA positions dataset",
      "object": "nba_clusts",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Position",
        "TurnoverPct",
        "ReboundPct",
        "AssistPct",
        "FieldGoalPct",
        "K1",
        "K2",
        "K3",
        "K4",
        "K5",
        "PC1",
        "PC2"
      ],
      "rows": 150,
      "table": true,
      "tojson": true
    },
    {
      "name": "sc_example",
      "title": "Simulated scRNA-seq dataset",
      "object": "sc_example",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "clustree-package",
      "title": "Clustree",
      "topics": [
        "clustree-package"
      ]
    },
    {
      "page": "clustree",
      "title": "Plot a clustering tree",
      "topics": [
        "clustree",
        "clustree.data.frame",
        "clustree.matrix",
        "clustree.Seurat",
        "clustree.seurat",
        "clustree.SingleCellExperiment"
      ]
    },
    {
      "page": "clustree_overlay",
      "title": "Overlay a clustering tree",
      "topics": [
        "clustree_overlay",
        "clustree_overlay.data.frame",
        "clustree_overlay.matrix",
        "clustree_overlay.Seurat",
        "clustree_overlay.seurat",
        "clustree_overlay.SingleCellExperiment"
      ]
    },
    {
      "page": "nba_clusts",
      "title": "Clustered NBA positions dataset",
      "topics": [
        "nba_clusts"
      ]
    },
    {
      "page": "sc_example",
      "title": "Simulated scRNA-seq dataset",
      "topics": [
        "sc_example"
      ]
    }
  ],
  "_pkglogo": "https://github.com/lazappi/clustree/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/lazappi/clustree/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "base64enc",
    "cachem",
    "checkmate",
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "fastmap",
    "generics",
    "ggforce",
    "ggplot2",
    "ggraph",
    "ggrepel",
    "glue",
    "graphlayouts",
    "gridExtra",
    "gtable",
    "igraph",
    "isoband",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "pillar",
    "pkgconfig",
    "polyclip",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "systemfonts",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tweenr",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "clustree.Rmd",
      "filename": "clustree.html",
      "title": "Plotting clustering trees",
      "author": "Luke Zappia",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What is a clustering tree?",
        "A simple example",
        "The data",
        "Plotting a tree",
        "Controlling aesthetics",
        "SC3 stability index",
        "Layout",
        "Adding labels",
        "Clustering trees for scRNA-seq data",
        "SingleCellExperiment objects",
        "Seurat objects",
        "Using genes as aesthetics",
        "Overlaying clustering trees",
        "Choosing what to colour",
        "Labelling nodes",
        "Showing the side view",
        "Modifying appearance",
        "Legends",
        "Citing clustree",
        "References"
      ],
      "created": "2018-01-22 05:02:31",
      "modified": "2023-11-05 17:51:20",
      "commits": 15
    }
  ],
  "_score": 11.846147937692086,
  "_indexed": true,
  "_nocasepkg": "clustree",
  "_universes": [
    "lazappi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.5.1",
      "date": "2026-06-04T10:24:36.000Z",
      "distro": "noble",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "919ad10ed3e8618d069739b38f5ea1b7d89b7601ee79e934b2de09b6c9d0132e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.5.1",
      "date": "2026-06-04T10:24:10.000Z",
      "distro": "noble",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "c0175eaceb14d092b3bfe3472767807b39aa0e155b7d511c9faebeb9378515bf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.5.1",
      "date": "2026-06-04T10:23:11.000Z",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "c5df32ca3f5ee713baf69f17c13b8a9c250661d309a5cc97b6570cd2c702cc6c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.5.1",
      "date": "2026-06-04T10:22:55.000Z",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "a70c2b6676268266545726ce653cf93df37b4d177cf4e4e02b438e52e6513c7b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.5.1",
      "date": "2026-06-04T10:24:30.000Z",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "16f758385f4e8225b6c1508adfef5efa7d0231a0a85851891a779fce6c786cb0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.5.1",
      "date": "2026-06-04T10:25:04.000Z",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "7f057c79bed274a4443b688406c48bc2fc9c7e4b66f03bf618ce39c2932d02c0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.5.1",
      "date": "2026-06-04T10:23:03.000Z",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "81561b4b69856c51eb91dc847fd2ae4d9a5852dc4d90f0c973ba7239e361f75a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.5.1",
      "date": "2026-06-04T10:23:06.000Z",
      "commit": "24900bdf459c29812c716ba9f889c58685f957ed",
      "fileid": "da7dfd204208799821da2c0d2553b884797f75342a28a22e3b3826fb87c5dc02",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lazappi/actions/runs/26945598751"
    }
  ]
}