{
  "_id": "6ad1ecb5a6a61792ed76c04e",
  "Package": "CancerEvolutionVisualization",
  "Title": "Publication Quality Phylogenetic Tree Plots",
  "Version": "3.0.0",
  "Date": "2025-06-13",
  "Authors@R": "c(\nperson(\"Paul Boutros\", role = \"cre\", email = \"PBoutros@mednet.ucla.edu\"),\nperson(\"Adriana Salcedo\", role = \"aut\"),\nperson(\"Dan Knight\", role = \"aut\"),\nperson(\"Helena Winata\", role = \"aut\"),\nperson(\"Selina Wu\", role = \"ctb\"))",
  "Description": "Generates tree plots with precise branch lengths, gene\nannotations, and cellular prevalence. The package handles\ncomplex tree structures (angles, lengths, etc.) and can be\nfurther refined as needed by the user.",
  "License": "GPL-2",
  "URL": "https://github.com/uclahs-cds/package-CancerEvolutionVisualization",
  "BugReports": "https://github.com/uclahs-cds/package-CancerEvolutionVisualization/issues",
  "VignetteBuilder": "knitr",
  "LazyLoad": "yes",
  "LazyData": "yes",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "libjpeg-dev libpng-dev",
  "Repository": "https://uclahs-cds.r-universe.dev",
  "Date/Publication": "2026-08-17 06:30:37 UTC",
  "RemoteUrl": "https://github.com/uclahs-cds/public-r-cancerevolutionvisualization",
  "RemoteRef": "HEAD",
  "RemoteSha": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-16 08:20:42 UTC",
    "User": "root"
  },
  "Author": "Paul Boutros [cre],\nAdriana Salcedo [aut],\nDan Knight [aut],\nHelena Winata [aut],\nSelina Wu [ctb]",
  "Maintainer": "Paul Boutros <PBoutros@mednet.ucla.edu>",
  "_user": "uclahs-cds",
  "_type": "src",
  "_file": "CancerEvolutionVisualization_3.0.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/23103a69e29e0c746037af964e82df651e456b38e7ef7521ba7fb3a3adaccf26",
  "_filesize": 8628029,
  "_sha256": "23103a69e29e0c746037af964e82df651e456b38e7ef7521ba7fb3a3adaccf26",
  "_expires": "2027-01-24T09:21:55.000Z",
  "_created": "2026-10-16T08:20:42.000Z",
  "_published": "2026-10-16T09:21:57.313Z",
  "_buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 116881662614,
      "time": 131,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "12034771025"
    },
    {
      "job": 116881662559,
      "time": 120,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12034461520"
    },
    {
      "job": 116881662450,
      "time": 123,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "12037385366"
    },
    {
      "job": 116881662390,
      "time": 137,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12036867496"
    },
    {
      "job": 116880381103,
      "time": 210,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12034850035"
    },
    {
      "job": 116881662603,
      "time": 110,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12034342725"
    },
    {
      "job": 116881662558,
      "time": 99,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "12034396629"
    },
    {
      "job": 116881662668,
      "time": 97,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "12034825680"
    },
    {
      "job": 116881662719,
      "time": 68,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12033937303"
    }
  ],
  "_upstream": "https://github.com/uclahs-cds/public-r-cancerevolutionvisualization",
  "_commit": {
    "id": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
    "author": "Helena Winata <hwinata@mednet.ucla.edu>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #191 from uclahs-cds/hwinata-fix-axis-regression\n\nRestore y-axes for non-default plotting directions and fix the linear fixture padding",
    "time": 1786948237
  },
  "_maintainer": {
    "name": "Paul Boutros",
    "email": "pboutros@mednet.ucla.edu",
    "login": "pboutros",
    "twitter": "@theboutroslab",
    "description": "",
    "uuid": 7833438
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Depends"
    },
    {
      "package": "grid",
      "role": "Depends"
    },
    {
      "package": "gridExtra",
      "role": "Depends"
    },
    {
      "package": "gtable",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BoutrosLab.plotting.general",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "uclahs-cds",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-20",
      "n": 2
    },
    {
      "week": "2026-34",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "dan-knight",
      "count": 692,
      "uuid": 56950335
    },
    {
      "user": "whelena",
      "count": 283,
      "uuid": 51138179
    },
    {
      "user": "asalcedo-bl",
      "count": 31,
      "uuid": 66493788
    },
    {
      "user": "aholmes",
      "count": 24,
      "uuid": 277061
    },
    {
      "user": "graceooh",
      "count": 8,
      "uuid": 53468028
    },
    {
      "user": "wuselina",
      "count": 3,
      "uuid": 68160979
    },
    {
      "user": "asalcedo31",
      "count": 2,
      "uuid": 8115145
    },
    {
      "user": "nwiltsie",
      "count": 2,
      "uuid": 829731
    },
    {
      "user": "tnyamaguchi",
      "count": 1,
      "uuid": 62572751
    }
  ],
  "_userbio": {
    "uuid": 61254633,
    "type": "organization",
    "name": "UCLA JCCC - Cancer Data Science",
    "followers": 46
  },
  "_downloads": {
    "count": 393,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CancerEvolutionVisualization"
  },
  "_devurl": "https://github.com/uclahs-cds/package-cancerevolutionvisualization",
  "_searchresults": 6,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/CancerEvolutionVisualization.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/uclahs-cds/public-r-cancerevolutionvisualization",
  "_realowner": "uclahs-cds",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2022-10-04"
    },
    {
      "version": "2.0.1",
      "date": "2023-11-21"
    }
  ],
  "_exports": [
    "create.ccf.densityplot",
    "create.ccf.heatmap",
    "create.ccf.summary.heatmap",
    "create.clone.genome.distribution.plot",
    "create.cluster.heatmap",
    "create.phylogenetic.tree",
    "data.frame.to.array",
    "get.colours.in.order",
    "SRCGrob",
    "update.descendant.property"
  ],
  "_datasets": [
    {
      "name": "colours",
      "title": "Colour scheme vector",
      "object": "colours",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "GRCh37",
      "title": "GRCh37 Chromosom Information",
      "object": "GRCh37",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "chr",
        "length",
        "UCSC_name"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "GRCh38",
      "title": "GRCh38 Chromosom Information",
      "object": "GRCh38",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "chr",
        "GC_Count",
        "GC_Percent",
        "length",
        "UCSC_name"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "snv",
      "title": "SNV dataframe",
      "object": "SNV",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "ID",
        "SNV.id",
        "CCF",
        "clone.id",
        "chr",
        "pos"
      ],
      "rows": 5401,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "colours",
      "title": "Colour scheme vector",
      "topics": [
        "colours"
      ]
    },
    {
      "page": "create.ccf.densityplot",
      "title": "CCF Density Plot",
      "topics": [
        "create.ccf.densityplot"
      ]
    },
    {
      "page": "create.ccf.heatmap",
      "title": "CCF Distribution Heatmap",
      "topics": [
        "create.ccf.heatmap"
      ]
    },
    {
      "page": "create.ccf.summary.heatmap",
      "title": "CCF Summary Heatmap",
      "topics": [
        "create.ccf.summary.heatmap"
      ]
    },
    {
      "page": "create.clone.genome.distribution.plot",
      "title": "Create Clone Genome Distribution Plot",
      "topics": [
        "create.clone.genome.distribution.plot"
      ]
    },
    {
      "page": "create.cluster.heatmap",
      "title": "Cluster Heatmap",
      "topics": [
        "create.cluster.heatmap"
      ]
    },
    {
      "page": "create.phylogenetic.tree",
      "title": "Phylogenetic Tree Plot",
      "topics": [
        "create.phylogenetic.tree"
      ]
    },
    {
      "page": "data.frame.to.array",
      "title": "Convert Data Frame to Array",
      "topics": [
        "data.frame.to.array"
      ]
    },
    {
      "page": "get.colours.in.order",
      "title": "Generate a named vector of colors for every value specified, ordered by the value in `value.order`.",
      "topics": [
        "get.colours.in.order"
      ]
    },
    {
      "page": "GRCh37",
      "title": "GRCh37 Chromosom Information",
      "topics": [
        "GRCh37"
      ]
    },
    {
      "page": "GRCh38",
      "title": "GRCh38 Chromosom Information",
      "topics": [
        "GRCh38"
      ]
    },
    {
      "page": "SNV",
      "title": "SNV dataframe",
      "topics": [
        "snv"
      ]
    },
    {
      "page": "SRCGrob",
      "title": "Subclone Tree Plot",
      "topics": [
        "SRCGrob"
      ]
    },
    {
      "page": "update.descendant.property",
      "title": "Update Tree Descendant Property",
      "topics": [
        "update.descendant.property"
      ]
    }
  ],
  "_readme": "https://github.com/uclahs-cds/public-r-cancerevolutionvisualization/raw/HEAD/README.md",
  "_rundeps": [
    "BoutrosLab.plotting.general",
    "class",
    "cli",
    "cluster",
    "deldir",
    "e1071",
    "glue",
    "gridExtra",
    "gtable",
    "hexbin",
    "interp",
    "jpeg",
    "lattice",
    "latticeExtra",
    "lifecycle",
    "MASS",
    "png",
    "proxy",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "rlang"
  ],
  "_vignettes": [
    {
      "source": "ManuscriptFigures.Rmd",
      "filename": "ManuscriptFigures.html",
      "title": "Reproducing Manuscript Figures",
      "author": "Helena Winata",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Figure 1: Multi-sample Analysis",
        "1B. CCF Heatmap",
        "1C. CCF Summary Heatmap",
        "1D. Clone Genome Distribution Plot",
        "1G. Multi-sample Phylogenetic Tree",
        "1G. Single-sample Phylogenetic Tree",
        "Figure 2: Phylogenetic tree features",
        "2A. Sample-specific subclones",
        "2B. Annotated single-sample phylogenetic tree",
        "2C. Mutation timeline tree",
        "2D. Radial mode with 2 edges",
        "2E. Dendrogram mode with 2 edges",
        "2F. Mixed mode with 2 edges",
        "2G. 500 node phylogentic tree"
      ],
      "created": "2024-12-10 21:31:25",
      "modified": "2026-01-23 23:57:51",
      "commits": 3
    },
    {
      "source": "UserGuide.Rmd",
      "filename": "UserGuide.html",
      "title": "CEV User Guide",
      "author": "Dan Knight, Helena Winata",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "CRAN (recommended)",
        "GitHub",
        "Basic Phylogenetic Tree Visualization",
        "Input Phylogenetic Data",
        "Simple Example",
        "Ex. 1.1: Minimal Tree",
        "Ex. 1.2: Using node.id, parent and label columns",
        "Ex. 1.3: Branch Lengths",
        "Ex. 1.4: Branch Scaling",
        "Ex. 1.5: Y-Axis Labels",
        "Ex. 1.6: Axis Tick Placement",
        "Ex. 1.7: Scale Bars",
        "Ex. 1.8: Visualizing Cellular Prevalence",
        "Customizing Node Arrangement",
        "Ex. 2.1: Node Spread",
        "Ex. 2.2: Node Angles",
        "Phylogenetic Tree Modes",
        "Ex. 3.1: Radial Mode",
        "Ex. 3.2: Dendrogram Mode",
        "Customizing Phylogenetic Tree Aesthetics",
        "Supported Aesthetic Input Columns",
        "Line Types",
        "Ex. 4.1: Styled Tree",
        "Ex. 4.2: Nodeless Tree",
        "Text Annotations",
        "Ex. 5.1: Edge annotations",
        "Ex. 5.2: Specifying Text Colour and Style",
        "Additional Plot Parameters",
        "Ex. 6.1: Adding the Normal Node",
        "Ex. 6.2: Horizontal Padding Between Tree and Axes",
        "Ex. 6.3: Plot Title",
        "Ex. 6.4: Saving Plot to file",
        "CCF Distribution Visualization",
        "Input SNV-to-subclone Assignment Data",
        "Ex. 7.1: CCF Distribution Heatmap",
        "Ex. 7.2: CCF Distribution Across subclones",
        "Ex. 7.3: Summary of CCF Distribution",
        "Ex. 7.4: Clone-Genome Distribution Plot"
      ],
      "created": "2022-08-02 00:29:38",
      "modified": "2024-12-16 19:45:01",
      "commits": 9
    }
  ],
  "_score": 5.8061799739838875,
  "_indexed": true,
  "_nocasepkg": "cancerevolutionvisualization",
  "_universes": [
    "uclahs-cds",
    "pboutros"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.0.0",
      "date": "2026-10-16T08:22:45.000Z",
      "distro": "resolute",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/de3ee14753a05fc34480f351ccaf71342fac625dc6e8249cb85bc5f978319cef",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.0.0",
      "date": "2026-10-16T08:22:49.000Z",
      "distro": "resolute",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/198e37a3508fdb84448c368075a5997ff48ccccff46d859c729ae2231765c929",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.0.0",
      "date": "2026-10-16T09:21:01.000Z",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/66df69076b1990242b0415e2ee4c6faa63003b8eb0327689bf9cbeb0d672e450",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.0.0",
      "date": "2026-10-16T09:19:13.000Z",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/9ec80c389d8a0d85983114fd71c4a18c947389baa18732a707c52262bc7eba58",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.0.0",
      "date": "2026-10-16T08:22:55.000Z",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/343270f5309b879e29b89bf509d4de4bda8f6d7cb27f53b96f59054530bf47ce",
      "status": "success",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.0.0",
      "date": "2026-10-16T08:22:00.000Z",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/cc5b5edc3253ae8150de3a71b79febbf6c31c145a134f3c3a5b3c1ac4e552640",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.0.0",
      "date": "2026-10-16T08:22:02.000Z",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/f9e5a1527be2222ca29e53822e95488981dfb983556145bafacaa45ce22edf64",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "3.0.0",
      "date": "2026-10-16T08:21:49.000Z",
      "commit": "9ba5dfb50a11dfe55412d5db8884f711dd8d6d32",
      "fileid": "https://r2.ropensci.org/25aa634a4fb079f85eb85991cee2fd6bf8b8cbc0c57a7e84c6d6a2846df0f545",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/uclahs-cds/actions/runs/38872688799"
    }
  ]
}