{
  "_id": "6a267f47794753ddbc3f0559",
  "Package": "circlizePlus",
  "Title": "Using 'ggplot2' Feature to Write Readable R Code for Circular\nVisualization",
  "Version": "0.9.1",
  "Authors@R": "c(\nperson(\"Tianze\", \"Cao\", , \"hnrcao@qq.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4308-1878\")),\nperson(\"Zheyu\", \"Zhang\", , \"2054906893@qq.com\", role = c(\"aut\"))\n)",
  "Description": "A wrapper for 'circlize'. All components are based on\nclasses and objects. Users can use the addition symbol (+) to\ncombine components for a circular visualization with 'ggplot2'\nstyle.The package is described in Zhang Z, Cao T, Huang Y and\nXia Y (2025) <doi:10.3389/fgene.2025.1535368>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Collate": "'track.R' 'heatmap.R' 'cell-geom.R' 'track-geom.R' 'link.R'\n'param.R' 'utils.R' 'initialize.R' 'add.R'\n'circlizePlus-package.R' 'data.R'",
  "Config/testthat/edition": "3",
  "URL": "https://github.com/TianzeLab/circlizePlus,\nhttps://tianzelab.github.io/circlizePlus/,\nhttps://doi.org/10.3389/fgene.2025.1535368",
  "BugReports": "https://github.com/TianzeLab/circlizePlus/issues",
  "VignetteBuilder": "knitr",
  "Repository": "https://tianzelab.r-universe.dev",
  "Date/Publication": "2025-05-23 09:08:05 UTC",
  "RemoteUrl": "https://github.com/tianzelab/circlizeplus",
  "RemoteRef": "HEAD",
  "RemoteSha": "2dd17670f42ce5f86b2cf73a9adc7cb6cf71d81a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 08:32:56 UTC",
    "User": "root"
  },
  "Author": "Tianze Cao [aut, cre] (ORCID: <https://orcid.org/0000-0003-4308-1878>),\nZheyu Zhang [aut]",
  "Maintainer": "Tianze Cao <hnrcao@qq.com>",
  "MD5sum": "617988891f994ace96a19821fbaf22f6",
  "_user": "tianzelab",
  "_type": "src",
  "_file": "circlizePlus_0.9.1.tar.gz",
  "_fileid": "d9db338bef1fd99d0ee2ca9d732f8638046a81861ae19d79bba3263df7c9969b",
  "_filesize": 3878064,
  "_sha256": "d9db338bef1fd99d0ee2ca9d732f8638046a81861ae19d79bba3263df7c9969b",
  "_created": "2026-06-08T08:32:56.000Z",
  "_published": "2026-06-08T08:37:27.175Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 80053174989,
      "time": 138,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7475166943"
    },
    {
      "job": 80053174988,
      "time": 137,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7475166242"
    },
    {
      "job": 80053174972,
      "time": 174,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
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    },
    {
      "job": 80053174969,
      "time": 232,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
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    },
    {
      "job": 80052693617,
      "time": 169,
      "config": "source",
      "r": "4.6.0",
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      "time": 109,
      "config": "wasm-release",
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      "artifact": "7475156649"
    },
    {
      "job": 80053174975,
      "time": 100,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7475153120"
    },
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      "job": 80053174986,
      "time": 104,
      "config": "windows-oldrel",
      "r": "4.5.3",
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    },
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      "time": 103,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7475155035"
    }
  ],
  "_buildurl": "https://github.com/r-universe/tianzelab/actions/runs/27125414449",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/tianzelab/circlizeplus",
  "_commit": {
    "id": "2dd17670f42ce5f86b2cf73a9adc7cb6cf71d81a",
    "author": "CaoTianze <hnrcao@qq.com>",
    "committer": "CaoTianze <hnrcao@qq.com>",
    "message": "Update CRAN-SUBMISSION\n",
    "time": 1747991285
  },
  "_maintainer": {
    "name": "Tianze Cao",
    "email": "hnrcao@qq.com",
    "login": "caotianze",
    "description": "\n",
    "uuid": 10096919,
    "orcid": "0000-0003-4308-1878"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "circlize",
      "version": ">= 0.4.16",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "png",
      "role": "Suggests"
    },
    {
      "package": "ape",
      "role": "Suggests"
    },
    {
      "package": "dendextend",
      "role": "Suggests"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "tianzelab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "circlize",
    "circular-visualization",
    "ggplot2"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "caotianze",
      "count": 153,
      "uuid": 10096919
    },
    {
      "user": "zzystc66",
      "count": 17,
      "uuid": 145750716
    }
  ],
  "_userbio": {
    "uuid": 145634701,
    "type": "organization",
    "name": "TianzeLab"
  },
  "_downloads": {
    "count": 554,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/circlizePlus"
  },
  "_devurl": "https://github.com/tianzelab/circlizeplus",
  "_pkgdown": "https://tianzelab.github.io/circlizePlus/",
  "_searchresults": 102,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/circlizePlus.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/tianzelab/circlizeplus",
  "_realowner": "tianzelab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.9.0",
      "date": "2025-04-22"
    },
    {
      "version": "0.9.1",
      "date": "2025-05-27"
    }
  ],
  "_exports": [
    "ccArrow",
    "ccBarplot",
    "ccBoxplot",
    "ccCell",
    "ccCells",
    "ccDendrogram",
    "ccGenomicAxis",
    "ccGenomicDensity",
    "ccGenomicHeatmap",
    "ccGenomicIdeogram",
    "ccGenomicLabels",
    "ccGenomicLines",
    "ccGenomicLink",
    "ccGenomicPoints",
    "ccGenomicRainfall",
    "ccGenomicRect",
    "ccGenomicText",
    "ccGenomicTrack",
    "ccHeatmap",
    "ccHeatmapLink",
    "ccLines",
    "ccLink",
    "ccPar",
    "ccPlot",
    "ccPoints",
    "ccPolygon",
    "ccRaster",
    "ccRect",
    "ccSegments",
    "ccText",
    "ccTrack",
    "ccTrackHist",
    "ccTrackLines",
    "ccTrackPoints",
    "ccTrackText",
    "ccViolin",
    "ccXaxis",
    "ccYaxis",
    "show"
  ],
  "_datasets": [
    {
      "name": "allele_frequency",
      "title": "Data set in circlizePlus",
      "object": "example2",
      "file": "example2.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Chromosome",
        "Start",
        "End",
        "Value"
      ],
      "rows": 25000,
      "table": true,
      "tojson": true
    },
    {
      "name": "copy_number",
      "title": "Data set in circlizePlus",
      "object": "example2",
      "file": "example2.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Chromosome",
        "Start",
        "End",
        "Value",
        "Array"
      ],
      "rows": 24788,
      "table": true,
      "tojson": true
    },
    {
      "name": "junctions",
      "title": "Data set in circlizePlus",
      "object": "example2",
      "file": "example2.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Id",
        "LeftChr",
        "LeftPosition",
        "LeftStrand",
        "LeftLength",
        "RightChr",
        "RightPosition",
        "RightStrand",
        "RightLength",
        "StrandConsistent",
        "Interchromosomal",
        "Distance",
        "DiscordantMatePairAlignments",
        "JunctionSequenceResolved",
        "TransitionSequence",
        "TransitionLength",
        "LeftRepeatClassification",
        "RightRepeatClassification",
        "LeftGenes",
        "RightGenes",
        "XRef",
        "DeletedTransposableElement",
        "KnownUnderrepresentedRepeat",
        "FrequencyInBaselineGenomeSet",
        "AssembledSequence",
        "EventId",
        "Type",
        "RelatedJunctions"
      ],
      "rows": 2414,
      "table": true,
      "tojson": true
    },
    {
      "name": "r1",
      "title": "Data set in circlizePlus",
      "object": "example2",
      "file": "example2.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrom",
        "chromStart",
        "chromEnd"
      ],
      "rows": 2414,
      "table": true,
      "tojson": true
    },
    {
      "name": "r2",
      "title": "Data set in circlizePlus",
      "object": "example2",
      "file": "example2.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrom",
        "chromStart",
        "chromEnd"
      ],
      "rows": 2414,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addition-rules",
      "title": "Addition rules in circlizePlus",
      "topics": [
        "+,ccCell,ccCellGeom-method",
        "+,ccCells,ccCellGeom-method",
        "+,ccHeatmap,ccLink-method",
        "+,ccHeatmap,ccPar-method",
        "+,ccHeatmap,ccTrack-method",
        "+,ccPlot,ccLink-method",
        "+,ccPlot,ccPar-method",
        "+,ccPlot,ccTrack-method",
        "+,ccTrack,ccCell-method",
        "+,ccTrack,ccCells-method",
        "+,ccTrack,ccTrackGeom-method",
        "addition-rules"
      ]
    },
    {
      "page": "ccArrow",
      "title": "Draw an arrow",
      "topics": [
        "ccArrow"
      ]
    },
    {
      "page": "ccBarplot",
      "title": "Draw barplots",
      "topics": [
        "ccBarplot"
      ]
    },
    {
      "page": "ccBoxplot",
      "title": "Draw boxplots",
      "topics": [
        "ccBoxplot"
      ]
    },
    {
      "page": "ccCell",
      "title": "Generate a cell container that belongs to a particular sector",
      "topics": [
        "ccCell"
      ]
    },
    {
      "page": "ccCell-class",
      "title": "S4 class ccCell",
      "topics": [
        "ccCell-class"
      ]
    },
    {
      "page": "ccCellGeom-class",
      "title": "S4 class ccCellGeom",
      "topics": [
        "ccCellGeom-class"
      ]
    },
    {
      "page": "ccCells",
      "title": "Generate a list of multiple object ccCell-class",
      "topics": [
        "ccCells"
      ]
    },
    {
      "page": "ccCells-class",
      "title": "S4 class ccCells",
      "topics": [
        "ccCells-class"
      ]
    },
    {
      "page": "ccDendrogram",
      "title": "Draw dendrogram plots in a track",
      "topics": [
        "ccDendrogram"
      ]
    },
    {
      "page": "ccGenomicAxis",
      "title": "Add genomic axes",
      "topics": [
        "ccGenomicAxis"
      ]
    },
    {
      "page": "ccGenomicCellGeom-class",
      "title": "S4 class ccGenomicCellGeom",
      "topics": [
        "ccGenomicCellGeom-class"
      ]
    },
    {
      "page": "ccGenomicDensity",
      "title": "Create a track of density plot",
      "topics": [
        "ccGenomicDensity"
      ]
    },
    {
      "page": "ccGenomicHeatmap",
      "title": "Define a heatmap track for genomic graph",
      "topics": [
        "ccGenomicHeatmap"
      ]
    },
    {
      "page": "ccGenomicIdeogram",
      "title": "Define an ideograms track for genomic graph",
      "topics": [
        "ccGenomicIdeogram"
      ]
    },
    {
      "page": "ccGenomicLabels",
      "title": "Add labels to specific genomic track",
      "topics": [
        "ccGenomicLabels"
      ]
    },
    {
      "page": "ccGenomicLines",
      "title": "Add lines for genomic data visualization",
      "topics": [
        "ccGenomicLines"
      ]
    },
    {
      "page": "ccGenomicLink",
      "title": "Add links between two sets of genomic positions",
      "topics": [
        "ccGenomicLink"
      ]
    },
    {
      "page": "ccGenomicLink-class",
      "title": "S4 class ccGenomicLink",
      "topics": [
        "ccGenomicLink-class"
      ]
    },
    {
      "page": "ccGenomicPoints",
      "title": "Add points for genomic data visualization",
      "topics": [
        "ccGenomicPoints"
      ]
    },
    {
      "page": "ccGenomicRainfall",
      "title": "Create a rainfall plot",
      "topics": [
        "ccGenomicRainfall"
      ]
    },
    {
      "page": "ccGenomicRect",
      "title": "Draw rectangle for genomic data visualization",
      "topics": [
        "ccGenomicRect"
      ]
    },
    {
      "page": "ccGenomicText",
      "title": "Add text for genomic data visualization",
      "topics": [
        "ccGenomicText"
      ]
    },
    {
      "page": "ccGenomicTrack",
      "title": "Define a track for genomic data visualization",
      "topics": [
        "ccGenomicTrack"
      ]
    },
    {
      "page": "ccGenomicTrack-class",
      "title": "S4 class ccGenomicTrack",
      "topics": [
        "ccGenomicTrack-class"
      ]
    },
    {
      "page": "ccHeatmap",
      "title": "Object generator for S4 class ccHeatmap",
      "topics": [
        "ccHeatmap"
      ]
    },
    {
      "page": "ccHeatmap-class",
      "title": "S4 class ccHeatmap",
      "topics": [
        "ccHeatmap-class"
      ]
    },
    {
      "page": "ccHeatmapLink",
      "title": "Draw a link between two matrix rows in the circular heatmap",
      "topics": [
        "ccHeatmapLink"
      ]
    },
    {
      "page": "ccHeatmapLink-class",
      "title": "S4 class ccHeatmapLink",
      "topics": [
        "ccHeatmapLink-class"
      ]
    },
    {
      "page": "ccLines",
      "title": "Draw lines in a region",
      "topics": [
        "ccLines"
      ]
    },
    {
      "page": "ccLink",
      "title": "Add a link",
      "topics": [
        "ccLink"
      ]
    },
    {
      "page": "ccLink-class",
      "title": "S4 class ccLink",
      "topics": [
        "ccLink-class"
      ]
    },
    {
      "page": "ccPar",
      "title": "Parameters for the circular layout",
      "topics": [
        "ccPar"
      ]
    },
    {
      "page": "ccPar-class",
      "title": "Object generator for S4 class ccPar",
      "topics": [
        "ccPar-class"
      ]
    },
    {
      "page": "ccPlot",
      "title": "Object generator for S4 class ccPlot",
      "topics": [
        "ccPlot"
      ]
    },
    {
      "page": "ccPlot-class",
      "title": "S4 class ccPlot",
      "topics": [
        "ccPlot-class"
      ]
    },
    {
      "page": "ccPoints",
      "title": "Draw points in a region",
      "topics": [
        "ccPoints"
      ]
    },
    {
      "page": "ccPolygon",
      "title": "Draw polygon",
      "topics": [
        "ccPolygon"
      ]
    },
    {
      "page": "ccRaster",
      "title": "Add raster image",
      "topics": [
        "ccRaster"
      ]
    },
    {
      "page": "ccRect",
      "title": "Draw rectangle in a region",
      "topics": [
        "ccRect"
      ]
    },
    {
      "page": "ccSegments",
      "title": "Draw segments connecting points in a region",
      "topics": [
        "ccSegments"
      ]
    },
    {
      "page": "ccText",
      "title": "Draw text in a cell",
      "topics": [
        "ccText"
      ]
    },
    {
      "page": "ccTrack",
      "title": "Define a generic track",
      "topics": [
        "ccTrack"
      ]
    },
    {
      "page": "ccTrack-class",
      "title": "S4 class ccTrack",
      "topics": [
        "ccTrack-class"
      ]
    },
    {
      "page": "ccTrackGeom-class",
      "title": "S4 class ccTrackGeom",
      "topics": [
        "ccTrackGeom-class"
      ]
    },
    {
      "page": "ccTrackHist",
      "title": "Define a track of histograms",
      "topics": [
        "ccTrackHist"
      ]
    },
    {
      "page": "ccTrackLines",
      "title": "Add lines on all sections of a single track.",
      "topics": [
        "ccTrackLines"
      ]
    },
    {
      "page": "ccTrackPoints",
      "title": "Add points on all sections of a single track.",
      "topics": [
        "ccTrackPoints"
      ]
    },
    {
      "page": "ccTrackText",
      "title": "Add texts on all sections of a single track.",
      "topics": [
        "ccTrackText"
      ]
    },
    {
      "page": "ccViolin",
      "title": "Draw violin plots",
      "topics": [
        "ccViolin"
      ]
    },
    {
      "page": "ccXaxis",
      "title": "Draw x-axis",
      "topics": [
        "ccXaxis"
      ]
    },
    {
      "page": "ccYaxis",
      "title": "Draw y-axis",
      "topics": [
        "ccYaxis"
      ]
    },
    {
      "page": "data-set",
      "title": "Data set in circlizePlus",
      "topics": [
        "allele_frequency",
        "copy_number",
        "data-set",
        "junctions",
        "r1",
        "r2"
      ]
    },
    {
      "page": "show-ccHeatmap-method",
      "title": "Draw the figures described by ccHeatmap",
      "topics": [
        "show,ccHeatmap-method"
      ]
    },
    {
      "page": "show-ccPlot-method",
      "title": "Draw the figures described by ccPlot",
      "topics": [
        "show,ccPlot-method"
      ]
    }
  ],
  "_readme": "https://github.com/tianzelab/circlizeplus/raw/HEAD/README.md",
  "_rundeps": [
    "circlize",
    "colorspace",
    "GlobalOptions",
    "shape"
  ],
  "_vignettes": [
    {
      "source": "example1.Rmd",
      "filename": "example1.html",
      "title": "Dot plot categorized by chromosome, and zoomed for partial chromosome categorization",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Code",
        "Step 1",
        "Step 2",
        "Step 3",
        "Step 4",
        "Step 5",
        "References"
      ],
      "created": "2025-05-22 06:25:35",
      "modified": "2025-05-23 08:43:11",
      "commits": 4
    },
    {
      "source": "example2.Rmd",
      "filename": "example2.html",
      "title": "Plot to present the VCaP cancer cell line",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Code",
        "References"
      ],
      "created": "2025-05-22 05:59:28",
      "modified": "2025-05-23 08:43:11",
      "commits": 3
    },
    {
      "source": "circlizePlus.Rmd",
      "filename": "circlizePlus.html",
      "title": "Using the circlizePlus Package",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Addition rules",
        "S4 class ccCell and ccCells",
        "API outline",
        "Initializer",
        "Parameter",
        "Cell container",
        "Cell geometry",
        "Track container",
        "Track geometry",
        "Link",
        "Heatmap",
        "Data mapping from track to cell geometry",
        "Get track from ccGenomicTrack()",
        "Get track from ccTrack()"
      ],
      "created": "2025-04-16 02:04:53",
      "modified": "2025-04-16 05:21:20",
      "commits": 3
    }
  ],
  "_score": 5.184691430817598,
  "_indexed": true,
  "_nocasepkg": "circlizeplus",
  "_universes": [
    "tianzelab",
    "caotianze"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.9.1",
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