{
  "_id": "6a16a354acfb0bcc41d81c96",
  "Package": "circlize",
  "Type": "Package",
  "Title": "Circular Visualization",
  "Version": "0.4.16",
  "Date": "2022-11-24",
  "Authors@R": "person(\"Zuguang\", \"Gu\", email = \"z.gu@dkfz.de\", role = c(\"aut\", \"cre\"),\ncomment = c('ORCID'=\"0000-0002-7395-8709\"))",
  "VignetteBuilder": "knitr",
  "Description": "Circular layout is an efficient way for the visualization\nof huge amounts of information. Here this package provides an\nimplementation of circular layout generation in R as well as an\nenhancement of available software. The flexibility of the\npackage is based on the usage of low-level graphics functions\nsuch that self-defined high-level graphics can be easily\nimplemented by users for specific purposes. Together with the\nseamless connection between the powerful computational and\nvisual environment in R, it gives users more convenience and\nfreedom to design figures for better understanding complex\npatterns behind multiple dimensional data. The package is\ndescribed in Gu et al. 2014\n<doi:10.1093/bioinformatics/btu393>.",
  "URL": "https://github.com/jokergoo/circlize,\nhttps://jokergoo.github.io/circlize_book/book/",
  "License": "MIT + file LICENSE",
  "Repository": "https://jokergoo.r-universe.dev",
  "Date/Publication": "2023-11-11 08:34:17 UTC",
  "RemoteUrl": "https://github.com/jokergoo/circlize",
  "RemoteRef": "HEAD",
  "RemoteSha": "9b2157843eba242f09adc66048e3470a1561f759",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 07:51:29 UTC",
    "User": "root"
  },
  "Author": "Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>)",
  "Maintainer": "Zuguang Gu <z.gu@dkfz.de>",
  "MD5sum": "3728a37cc2cb3e04d1ee0ea70478104a",
  "_user": "jokergoo",
  "_type": "src",
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  "_created": "2026-05-27T07:51:29.000Z",
  "_published": "2026-05-27T07:55:00.470Z",
  "_distro": "noble",
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    "message": "Create CODE_OF_CONDUCT.md",
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  "_homeurl": "https://github.com/jokergoo/circlize",
  "_realowner": "jokergoo",
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  ],
  "_exports": [
    "$.CELL_META",
    "add_transparency",
    "adjacencyList2Matrix",
    "adjacencyMatrix2List",
    "arrange_links_evenly",
    "calc_gap",
    "CELL_META",
    "chordDiagram",
    "chordDiagramFromDataFrame",
    "chordDiagramFromMatrix",
    "circlize",
    "circos.arrow",
    "circos.axis",
    "circos.barplot",
    "circos.boxplot",
    "circos.clear",
    "circos.connect",
    "circos.dendrogram",
    "circos.genomicAxis",
    "circos.genomicDensity",
    "circos.genomicHeatmap",
    "circos.genomicIdeogram",
    "circos.genomicInitialize",
    "circos.genomicLabels",
    "circos.genomicLines",
    "circos.genomicLink",
    "circos.genomicPoints",
    "circos.genomicPosTransformLines",
    "circos.genomicRainfall",
    "circos.genomicRect",
    "circos.genomicText",
    "circos.genomicTrack",
    "circos.genomicTrackPlotRegion",
    "circos.heatmap",
    "circos.heatmap.get.x",
    "circos.heatmap.initialize",
    "circos.heatmap.link",
    "circos.info",
    "circos.initialize",
    "circos.initializeCircularGenome",
    "circos.initializeWithIdeogram",
    "circos.labels",
    "circos.lines",
    "circos.link",
    "circos.nested",
    "circos.par",
    "circos.points",
    "circos.polygon",
    "circos.raster",
    "circos.rect",
    "circos.segments",
    "circos.stackedText",
    "circos.text",
    "circos.track",
    "circos.trackHist",
    "circos.trackLines",
    "circos.trackPlotRegion",
    "circos.trackPoints",
    "circos.trackText",
    "circos.triangle",
    "circos.update",
    "circos.updatePlotRegion",
    "circos.violin",
    "circos.xaxis",
    "circos.yaxis",
    "cm_h",
    "cm_x",
    "cm_y",
    "col2value",
    "colorRamp2",
    "convert_height",
    "convert_length",
    "convert_x",
    "convert_y",
    "cytoband.col",
    "degree",
    "draw.sector",
    "fontsize",
    "generateRandomBed",
    "genomicDensity",
    "get_most_inside_radius",
    "get.all.sector.index",
    "get.all.track.index",
    "get.cell.meta.data",
    "get.current.chromosome",
    "get.current.sector.index",
    "get.current.track.index",
    "getI",
    "highlight.chromosome",
    "highlight.sector",
    "inch_h",
    "inch_x",
    "inch_y",
    "inches_h",
    "inches_x",
    "inches_y",
    "mm_h",
    "mm_x",
    "mm_y",
    "names.CELL_META",
    "posTransform.default",
    "posTransform.text",
    "print.CELL_META",
    "rainfallTransform",
    "rand_color",
    "read.chromInfo",
    "read.cytoband",
    "reverse.circlize",
    "set_track_gap",
    "set.current.cell",
    "show.index",
    "smartAlign",
    "uh",
    "ux",
    "uy"
  ],
  "_help": [
    {
      "page": "circlize-package",
      "title": "Circular visualization in R",
      "topics": [
        "circlize-package"
      ]
    },
    {
      "page": "Subset.CELL_META",
      "title": "Easy to way to get meta data in the current cell",
      "topics": [
        "$.CELL_META",
        "Subset.CELL_META"
      ]
    },
    {
      "page": "add_transparency",
      "title": "Add transparency to colors",
      "topics": [
        "add_transparency"
      ]
    },
    {
      "page": "adjacencyList2Matrix",
      "title": "Convert adjacency list to an adjacency matrix",
      "topics": [
        "adjacencyList2Matrix"
      ]
    },
    {
      "page": "adjacencyMatrix2List",
      "title": "Convert adjacency matrix to an adjacency list",
      "topics": [
        "adjacencyMatrix2List"
      ]
    },
    {
      "page": "arrange_links_evenly",
      "title": "Arrange links evenly on each sector",
      "topics": [
        "arrange_links_evenly"
      ]
    },
    {
      "page": "calc_gap",
      "title": "Calculate gaps to make two Chord diagrams in the same scale",
      "topics": [
        "calc_gap"
      ]
    },
    {
      "page": "CELL_META",
      "title": "Easy way to get meta data in the current cell",
      "topics": [
        "CELL_META"
      ]
    },
    {
      "page": "chordDiagram",
      "title": "Plot Chord Diagram",
      "topics": [
        "chordDiagram"
      ]
    },
    {
      "page": "chordDiagramFromDataFrame",
      "title": "Plot Chord Diagram from a data frame",
      "topics": [
        "chordDiagramFromDataFrame"
      ]
    },
    {
      "page": "chordDiagramFromMatrix",
      "title": "Plot Chord Diagram from an adjacency matrix",
      "topics": [
        "chordDiagramFromMatrix"
      ]
    },
    {
      "page": "circlize",
      "title": "Convert to polar coordinate system",
      "topics": [
        "circlize"
      ]
    },
    {
      "page": "circos.arrow",
      "title": "Draw arrow which is paralle to the circle",
      "topics": [
        "circos.arrow"
      ]
    },
    {
      "page": "circos.axis",
      "title": "Draw x-axis",
      "topics": [
        "circos.axis"
      ]
    },
    {
      "page": "circos.barplot",
      "title": "Draw barplots",
      "topics": [
        "circos.barplot"
      ]
    },
    {
      "page": "circos.boxplot",
      "title": "Draw boxplots",
      "topics": [
        "circos.boxplot"
      ]
    },
    {
      "page": "circos.clear",
      "title": "Reset the circular layout parameters",
      "topics": [
        "circos.clear"
      ]
    },
    {
      "page": "circos.connect",
      "title": "Draw connecting lines/ribons between two sets of points",
      "topics": [
        "circos.connect"
      ]
    },
    {
      "page": "circos.dendrogram",
      "title": "Add circular dendrograms",
      "topics": [
        "circos.dendrogram"
      ]
    },
    {
      "page": "circos.genomicAxis",
      "title": "Add genomic axes",
      "topics": [
        "circos.genomicAxis"
      ]
    },
    {
      "page": "circos.genomicDensity",
      "title": "Calculate and add genomic density track",
      "topics": [
        "circos.genomicDensity"
      ]
    },
    {
      "page": "circos.genomicHeatmap",
      "title": "Add heatmaps for selected regions",
      "topics": [
        "circos.genomicHeatmap"
      ]
    },
    {
      "page": "circos.genomicIdeogram",
      "title": "Add an ideogram track",
      "topics": [
        "circos.genomicIdeogram"
      ]
    },
    {
      "page": "circos.genomicInitialize",
      "title": "Initialize circular plot with any genomic data",
      "topics": [
        "circos.genomicInitialize"
      ]
    },
    {
      "page": "circos.genomicLabels",
      "title": "Add labels to specified genomic regions",
      "topics": [
        "circos.genomicLabels"
      ]
    },
    {
      "page": "circos.genomicLines",
      "title": "Add lines to a plotting region, specifically for genomic graphics",
      "topics": [
        "circos.genomicLines"
      ]
    },
    {
      "page": "circos.genomicLink",
      "title": "Add links from two sets of genomic positions",
      "topics": [
        "circos.genomicLink"
      ]
    },
    {
      "page": "circos.genomicPoints",
      "title": "Add points to a plotting region, specifically for genomic graphics",
      "topics": [
        "circos.genomicPoints"
      ]
    },
    {
      "page": "circos.genomicPosTransformLines",
      "title": "Add genomic position transformation lines between tracks",
      "topics": [
        "circos.genomicPosTransformLines"
      ]
    },
    {
      "page": "circos.genomicRainfall",
      "title": "Genomic rainfall plot",
      "topics": [
        "circos.genomicRainfall"
      ]
    },
    {
      "page": "circos.genomicRect",
      "title": "Draw rectangle-like grid, specifically for genomic graphics",
      "topics": [
        "circos.genomicRect"
      ]
    },
    {
      "page": "circos.genomicText",
      "title": "Draw text in a cell, specifically for genomic graphics",
      "topics": [
        "circos.genomicText"
      ]
    },
    {
      "page": "circos.genomicTrack",
      "title": "Create a track for genomic graphics",
      "topics": [
        "circos.genomicTrack"
      ]
    },
    {
      "page": "circos.genomicTrackPlotRegion",
      "title": "Create a track for genomic graphics",
      "topics": [
        "circos.genomicTrackPlotRegion"
      ]
    },
    {
      "page": "circos.heatmap",
      "title": "Make circular heatmaps",
      "topics": [
        "circos.heatmap"
      ]
    },
    {
      "page": "circos.heatmap.get.x",
      "title": "Get the x-position for heatmap rows",
      "topics": [
        "circos.heatmap.get.x"
      ]
    },
    {
      "page": "circos.heatmap.initialize",
      "title": "Initialize circular heatmaps",
      "topics": [
        "circos.heatmap.initialize"
      ]
    },
    {
      "page": "circos.heatmap.link",
      "title": "Draw a link between two matrix rows in the circular heatmap",
      "topics": [
        "circos.heatmap.link"
      ]
    },
    {
      "page": "circos.info",
      "title": "Get information of the circular plot",
      "topics": [
        "circos.info"
      ]
    },
    {
      "page": "circos.initialize",
      "title": "Initialize the circular layout",
      "topics": [
        "circos.initialize"
      ]
    },
    {
      "page": "circos.initializeCircularGenome",
      "title": "Initialize a layout for circular genome",
      "topics": [
        "circos.initializeCircularGenome"
      ]
    },
    {
      "page": "circos.initializeWithIdeogram",
      "title": "Initialize the circular layout with an ideogram",
      "topics": [
        "circos.initializeWithIdeogram"
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    {
      "page": "circos.labels",
      "title": "Add a label track",
      "topics": [
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    },
    {
      "page": "circos.lines",
      "title": "Add lines to the plotting region",
      "topics": [
        "circos.lines"
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    },
    {
      "page": "circos.link",
      "title": "Draw links between points or/and intervals",
      "topics": [
        "circos.link"
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    },
    {
      "page": "circos.nested",
      "title": "Nested zooming with two circular plots",
      "topics": [
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    },
    {
      "page": "circos.par",
      "title": "Parameters for the circular layout",
      "topics": [
        "circos.par"
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    },
    {
      "page": "circos.points",
      "title": "Add points to a plotting region",
      "topics": [
        "circos.points"
      ]
    },
    {
      "page": "circos.polygon",
      "title": "Draw polygon",
      "topics": [
        "circos.polygon"
      ]
    },
    {
      "page": "circos.raster",
      "title": "Add raster images",
      "topics": [
        "circos.raster"
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    },
    {
      "page": "circos.rect",
      "title": "Draw rectangle-like grid",
      "topics": [
        "circos.rect"
      ]
    },
    {
      "page": "circos.segments",
      "title": "Draw segments through pairwise of points",
      "topics": [
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    },
    {
      "page": "circos.stackedText",
      "title": "Add a stacked text track",
      "topics": [
        "circos.stackedText"
      ]
    },
    {
      "page": "circos.text",
      "title": "Draw text in a cell",
      "topics": [
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    },
    {
      "page": "circos.track",
      "title": "Create plotting regions for a whole track",
      "topics": [
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    },
    {
      "page": "circos.trackHist",
      "title": "Draw histogram in cells among a whole track",
      "topics": [
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    },
    {
      "page": "circos.trackLines",
      "title": "Add lines to the plotting regions in a same track",
      "topics": [
        "circos.trackLines"
      ]
    },
    {
      "page": "circos.trackPlotRegion",
      "title": "Create plotting regions for a whole track",
      "topics": [
        "circos.trackPlotRegion"
      ]
    },
    {
      "page": "circos.trackPoints",
      "title": "Add points to the plotting regions in a same track",
      "topics": [
        "circos.trackPoints"
      ]
    },
    {
      "page": "circos.trackText",
      "title": "Draw text in cells among the whole track",
      "topics": [
        "circos.trackText"
      ]
    },
    {
      "page": "circos.triangle",
      "title": "Draw triangles",
      "topics": [
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      ]
    },
    {
      "page": "circos.update",
      "title": "Create plotting regions for a whole track",
      "topics": [
        "circos.update"
      ]
    },
    {
      "page": "circos.updatePlotRegion",
      "title": "Update the plotting region in an existed cell",
      "topics": [
        "circos.updatePlotRegion"
      ]
    },
    {
      "page": "circos.violin",
      "title": "Draw violin plots",
      "topics": [
        "circos.violin"
      ]
    },
    {
      "page": "circos.xaxis",
      "title": "Draw x-axis",
      "topics": [
        "circos.xaxis"
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    },
    {
      "page": "circos.yaxis",
      "title": "Draw y-axis",
      "topics": [
        "circos.yaxis"
      ]
    },
    {
      "page": "cm_h",
      "title": "Convert units",
      "topics": [
        "cm_h"
      ]
    },
    {
      "page": "cm_x",
      "title": "Convert unit on x direction in data coordinate",
      "topics": [
        "cm_x"
      ]
    },
    {
      "page": "cm_y",
      "title": "Convert unit on y direction in data coordinate",
      "topics": [
        "cm_y"
      ]
    },
    {
      "page": "col2value",
      "title": "Transform back from colors to values",
      "topics": [
        "col2value"
      ]
    },
    {
      "page": "colorRamp2",
      "title": "Color interpolation",
      "topics": [
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      ]
    },
    {
      "page": "convert_height",
      "title": "Convert units",
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      "page": "convert_length",
      "title": "Convert units",
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    {
      "page": "convert_x",
      "title": "Convert unit on x direction in data coordinate",
      "topics": [
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    {
      "page": "convert_y",
      "title": "Convert unit on y direction in data coordinate",
      "topics": [
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    },
    {
      "page": "cytoband.col",
      "title": "Assign colors to cytogenetic band (hg19) according to the Giemsa stain results",
      "topics": [
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    },
    {
      "page": "degree",
      "title": "Mark the value as a degree value",
      "topics": [
        "degree"
      ]
    },
    {
      "page": "draw.sector",
      "title": "Draw sectors or rings in a circle",
      "topics": [
        "draw.sector"
      ]
    },
    {
      "page": "fontsize",
      "title": "Convert fontsize to cex",
      "topics": [
        "fontsize"
      ]
    },
    {
      "page": "generateRandomBed",
      "title": "Generate random genomic data",
      "topics": [
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      ]
    },
    {
      "page": "genomicDensity",
      "title": "Calculate genomic region density",
      "topics": [
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    },
    {
      "page": "get_most_inside_radius",
      "title": "Get the inside radius of the most inner track",
      "topics": [
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    },
    {
      "page": "get.all.sector.index",
      "title": "Get index for all sectors",
      "topics": [
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    },
    {
      "page": "get.all.track.index",
      "title": "Get index for all tracks",
      "topics": [
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    },
    {
      "page": "get.cell.meta.data",
      "title": "Get the meta data of a cell",
      "topics": [
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    },
    {
      "page": "get.current.chromosome",
      "title": "Get current chromosome name",
      "topics": [
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    },
    {
      "page": "get.current.sector.index",
      "title": "Get current sector index",
      "topics": [
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    },
    {
      "page": "get.current.track.index",
      "title": "Get current track index",
      "topics": [
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    },
    {
      "page": "getI",
      "title": "Which data that 'panel.fun' is using",
      "topics": [
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    },
    {
      "page": "highlight.chromosome",
      "title": "Highlight chromosomes",
      "topics": [
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    },
    {
      "page": "highlight.sector",
      "title": "Highlight sectors and tracks",
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      "page": "inch_h",
      "title": "Convert units",
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      "page": "inch_x",
      "title": "Convert unit on x direction in data coordinate",
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      "page": "inch_y",
      "title": "Convert unit on y direction in data coordinate",
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      "page": "inches_h",
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      "page": "inches_y",
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      "page": "mm_h",
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      "topics": [
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    },
    {
      "page": "mm_x",
      "title": "Convert unit on x direction in data coordinate",
      "topics": [
        "mm_x"
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    {
      "page": "mm_y",
      "title": "Convert unit on y direction in data coordinate",
      "topics": [
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    },
    {
      "page": "names.CELL_META",
      "title": "Names of all meta data in the current cell",
      "topics": [
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    },
    {
      "page": "posTransform.default",
      "title": "Genomic position transformation function",
      "topics": [
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    },
    {
      "page": "posTransform.text",
      "title": "Genomic position transformation function specifically for text",
      "topics": [
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      "page": "print.CELL_META",
      "title": "Print CELL_META",
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    {
      "page": "rainfallTransform",
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      "page": "rand_color",
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    {
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      "page": "show.index",
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      "page": "smartAlign",
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      "page": "uh",
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        "ux"
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