{
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  "Package": "plotgardener",
  "Title": "Coordinate-Based Genomic Visualization Package for R",
  "Version": "1.19.0",
  "Date": "2024-06-28",
  "Author": "Nicole Kramer [aut, cre], Eric S. Davis [aut], Craig Wenger\n[aut], Sarah Parker [ctb], Erika Deoudes [art], Michael Love\n[ctb], Douglas H. Phanstiel [aut, cre, cph]",
  "Maintainer": "Nicole Kramer <nekramer27@gmail.com>, Douglas Phanstiel\n<douglas_phanstiel@med.unc.edu>",
  "Description": "Coordinate-based genomic visualization package for R. It\ngrants users the ability to programmatically produce complex,\nmulti-paneled figures. Tailored for genomics, plotgardener\nallows users to visualize large complex genomic datasets and\nprovides exquisite control over how plots are placed and\narranged on a page.",
  "License": "MIT + file LICENSE",
  "URL": "https://phanstiellab.github.io/plotgardener,\nhttps://github.com/PhanstielLab/plotgardener",
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  "RoxygenNote": "7.3.2",
  "biocViews": "Visualization, GenomeAnnotation, FunctionalGenomics,\nGenomeAssembly, HiC",
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  "BugReports": "https://github.com/PhanstielLab/plotgardener/issues",
  "Config/pak/sysreqs": "cmake make libbz2-dev liblzma-dev libuv1-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:46 UTC",
  "RemoteUrl": "https://github.com/bioc/plotgardener",
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    "calcSignalRange",
    "colorby",
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    "pageCreate",
    "pageGuideHide",
    "pageGuideHorizontal",
    "pageGuideShow",
    "pageGuideVertical",
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    "plotGenes",
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    "plotLegend",
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    "plotMultiSignal",
    "plotPairs",
    "plotPairsArches",
    "plotPolygon",
    "plotRanges",
    "plotRaster",
    "plotRect",
    "plotSegments",
    "plotSignal",
    "plotText",
    "plotTranscripts",
    "readBigwig",
    "readCool",
    "readCoolBpResolutions",
    "readCoolChroms",
    "readCoolNorms",
    "readHic"
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      "title": "Check for .(m)cool file and contents",
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      "topics": [
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      "topics": [
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      "topics": [
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    {
      "page": "pageGuideShow",
      "title": "Reshow guides drawn with 'pageCreate', 'pageGuideHorizontal', and 'pageGuideVertical'",
      "topics": [
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      ]
    },
    {
      "page": "pageGuideVertical",
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      "topics": [
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      ]
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      "topics": [
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      "title": "Generate row positions for a number of plot elements with a specified height and space between them",
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      "title": "pgParams: plotgardener parameters object",
      "topics": [
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    {
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      "title": "plotgardener: Coordinate-based Genomic Visualization Package for R",
      "topics": [
        "plotgardener-package",
        "plotgardener"
      ]
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      "page": "plotGenes",
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      "topics": [
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      ]
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    {
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      "title": "Plot genomic coordinates along the x or y-axis of a plotgardener plot",
      "topics": [
        "plotGenomeLabel"
      ]
    },
    {
      "page": "plotGG",
      "title": "Plot a ggplot2 plot, gtable, or grob object in a plotgardener layout",
      "topics": [
        "plotGG"
      ]
    },
    {
      "page": "plotHicRectangle",
      "title": "Plot a triangular Hi-C interaction matrix in a rectangular format",
      "topics": [
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      ]
    },
    {
      "page": "plotHicSquare",
      "title": "Plot a Hi-C interaction matrix in a square format",
      "topics": [
        "plotHicSquare"
      ]
    },
    {
      "page": "plotHicTriangle",
      "title": "Plot a Hi-C interaction matrix in a triangular format",
      "topics": [
        "plotHicTriangle"
      ]
    },
    {
      "page": "plotIdeogram",
      "title": "Plot a chromosome ideogram with or without cytobands",
      "topics": [
        "plotIdeogram"
      ]
    },
    {
      "page": "plotLegend",
      "title": "Plot a legend",
      "topics": [
        "plotLegend"
      ]
    },
    {
      "page": "plotManhattan",
      "title": "Plot a Manhattan plot",
      "topics": [
        "plotManhattan"
      ]
    },
    {
      "page": "plotMultiSignal",
      "title": "Plot multiple signal tracks in line with each other",
      "topics": [
        "plotMultiSignal"
      ]
    },
    {
      "page": "plotPairs",
      "title": "Plot paired-end genomic range elements",
      "topics": [
        "plotPairs"
      ]
    },
    {
      "page": "plotPairsArches",
      "title": "Plot paired-end genomic range data in an arch style",
      "topics": [
        "plotPairsArches"
      ]
    },
    {
      "page": "plotPolygon",
      "title": "Plot a polygon within a plotgardener layout",
      "topics": [
        "plotPolygon"
      ]
    },
    {
      "page": "plotRanges",
      "title": "Plot genomic range elements in a pileup or collapsed format",
      "topics": [
        "plotRanges"
      ]
    },
    {
      "page": "plotRaster",
      "title": "Plot a raster object within a plotgardener layout",
      "topics": [
        "plotRaster"
      ]
    },
    {
      "page": "plotRect",
      "title": "Plot a rectangle within a plotgardener layout",
      "topics": [
        "plotRect"
      ]
    },
    {
      "page": "plotSegments",
      "title": "Draw a line segment within a plotgardener layout",
      "topics": [
        "plotSegments"
      ]
    },
    {
      "page": "plotSignal",
      "title": "Plot any kind of signal track data for a single chromosome",
      "topics": [
        "plotSignal"
      ]
    },
    {
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