{
  "_id": "6a1efedcb401979e7341a858",
  "Package": "ribiosPlot",
  "Type": "Package",
  "Title": "Plotting Module of the 'ribios' Software Suite",
  "Version": "1.3.0",
  "Date": "2026-02-20",
  "Authors@R": "c(person(given = \"Jitao David\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cre\", \"ctb\"),\nemail = \"jitao_david.zhang@roche.com\",\ncomment = c(ORCID=\"0000-0002-3085-0909\")))",
  "Description": "Provides data structures and functions for data\ntransformation and visualization in computational biology in\ndrug discovery as part of the 'ribios' software suite. Zhang\n(2025) <https://github.com/bedapub/ribiosPlot>.",
  "Collate": "AllClasses.R AllMethods.R utils.R ribiosPlot-package.R\nrobustdist.R p2asterisk.R ellipse.R colors.R fcol.R hist.R\njitter.xyplot.R compactTrellis.R cascadePlot.R biosHeatmap.R\nPCAScoreMatrix.R expVar.R pcaPlots.R plotVenn.R pairs.R\nfigurePanel.R ggSmoothScatter.R openFileDevice.R vennMembers.R",
  "License": "GPL-3",
  "URL": "https://github.com/bedapub/ribiosPlot",
  "BugReports": "https://github.com/bedapub/ribiosPlot/issues",
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  "Additional_repositories": "https://bedapub.r-universe.dev",
  "Repository": "https://bedapub.r-universe.dev",
  "Date/Publication": "2026-02-20 21:11:39 UTC",
  "RemoteUrl": "https://github.com/bedapub/ribiosPlot",
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  "Packaged": {
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    "User": "root"
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  "Author": "Jitao David Zhang [aut, cre, ctb] (ORCID:\n<https://orcid.org/0000-0002-3085-0909>)",
  "Maintainer": "Jitao David Zhang <jitao_david.zhang@roche.com>",
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  "_exports": [
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    "blackgreen",
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    "blackredyellow",
    "blackwhite",
    "blackyellow",
    "blueblackred",
    "bluered",
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    "boundNorm",
    "brewer.pal.factor",
    "cascadeOrder",
    "closeFileDevice",
    "colorpanel",
    "compactPar",
    "compactTrellis",
    "confEllipse",
    "cyanblackyellow",
    "degree2radian",
    "display.colorpanels",
    "display.threecolor.panels",
    "display.twocolor.panels",
    "ellipse",
    "expVar",
    "expVarLabel",
    "fcbase",
    "fcbase<-",
    "fcbrewer",
    "fcol",
    "figurePanel",
    "getDefaultFontFamily",
    "getExpVarLabel",
    "getLims",
    "greenred",
    "guessWH",
    "heat",
    "histMat",
    "idev",
    "intRange",
    "ipdf",
    "jitter.xyplot",
    "magentayellow",
    "midCol",
    "nonNull",
    "openFileDevice",
    "p2asterisk",
    "panel.cor",
    "panel.lmSmooth",
    "PCAScoreMatrix",
    "pcaScores",
    "pcaScoresFromLogFC",
    "pdf2png",
    "plotPCA",
    "plotPCAloading",
    "plotVenn",
    "qBreaks",
    "qHist",
    "radian2degree",
    "redblackblue",
    "redblue",
    "redgreen",
    "robustDist",
    "rowVars",
    "royalbluegrayred",
    "royalbluered",
    "royalredblue",
    "royalredgrayblue",
    "setCompactTrellis",
    "squareLayout",
    "symrange",
    "threecolor.panels",
    "turyeb",
    "twocolor.panels",
    "vennMembersDataframe",
    "vennMembersList",
    "whiteblack",
    "whiteblue",
    "whiteblueblackheat",
    "whitered",
    "xclipHist",
    "yellowblack",
    "yellowblackcyan",
    "yellowmagenta"
  ],
  "_help": [
    {
      "page": "sub-.PCAScoreMatrix",
      "title": "Subsetting PCAScoreMatrix while keeping the expVar attribute",
      "topics": [
        "[.PCAScoreMatrix"
      ]
    },
    {
      "page": "as.data.frame.PCAScoreMatrix",
      "title": "Coerece a PCAScoreMatrix into data.frame",
      "topics": [
        "as.data.frame.PCAScoreMatrix"
      ]
    },
    {
      "page": "as.matrix.PCAScoreMatrix",
      "title": "Coerece a PCAScoreMatrix into score matrix",
      "topics": [
        "as.matrix.PCAScoreMatrix"
      ]
    },
    {
      "page": "biosHeatmap",
      "title": "CUSTOMED HEATMAP.2 FOR BIOS USERS",
      "topics": [
        "biosHeatmap"
      ]
    },
    {
      "page": "brewer.pal.factor",
      "title": "Build brewer.pal colors from factor (Deprecated)",
      "topics": [
        "brewer.pal.factor",
        "brewer.pal.factorLevels"
      ]
    },
    {
      "page": "cascadeOrder",
      "title": "Order rows of a matrix in the cascade order",
      "topics": [
        "cascadeOrder"
      ]
    },
    {
      "page": "colorpanel",
      "title": "Generates a set of colors that varies smoothly.",
      "topics": [
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      ]
    },
    {
      "page": "compactPar",
      "title": "Compact par setting",
      "topics": [
        "compactPar"
      ]
    },
    {
      "page": "compactTrellis",
      "title": "Return a compact setting for lattice plots, useful for preparing publications",
      "topics": [
        "compactTrellis"
      ]
    },
    {
      "page": "confEllipse",
      "title": "Plot confidence ellipse based on two-dimenstional data",
      "topics": [
        "confEllipse"
      ]
    },
    {
      "page": "degree2radian",
      "title": "Convert degree to radian values",
      "topics": [
        "degree2radian"
      ]
    },
    {
      "page": "display.colorpanels",
      "title": "Display color panels",
      "topics": [
        "display.colorpanels"
      ]
    },
    {
      "page": "display.threecolor.panels",
      "title": "Display three-color panels",
      "topics": [
        "display.threecolor.panels"
      ]
    },
    {
      "page": "display.twocolor.panels",
      "title": "Display two-color panels",
      "topics": [
        "display.twocolor.panels"
      ]
    },
    {
      "page": "ellipse",
      "title": "Add an ellipse in an existing plot",
      "topics": [
        "ellipse"
      ]
    },
    {
      "page": "expVar",
      "title": "S3 function expVar to extract explained variance from prcomp and PCAScoreMatrix objects",
      "topics": [
        "expVar",
        "expVar.PCAScoreMatrix",
        "expVar.prcomp"
      ]
    },
    {
      "page": "expVarLabel",
      "title": "Generic function expVarLabel to generate a label of explained variance from prcomp and PCAScoreMatrix objects",
      "topics": [
        "expVarLabel"
      ]
    },
    {
      "page": "expVarLabel.PCAScoreMatrix",
      "title": "Labels of principal components from PCAScoreMatrix",
      "topics": [
        "expVarLabel.PCAScoreMatrix"
      ]
    },
    {
      "page": "expVarLabel.prcomp",
      "title": "Labels of principal components from prcomp",
      "topics": [
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      ]
    },
    {
      "page": "fcbase",
      "title": "Return base colors of a fcol object",
      "topics": [
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      ]
    },
    {
      "page": "fcbase-set",
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      "topics": [
        "fcbase<-"
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    },
    {
      "page": "fcbrewer",
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        "fcbrewer"
      ]
    },
    {
      "page": "fcol",
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      "topics": [
        "fcol"
      ]
    },
    {
      "page": "figurePanel",
      "title": "Make a figure panel with title",
      "topics": [
        "figurePanel"
      ]
    },
    {
      "page": "getDefaultFontFamily",
      "title": "Get default font family",
      "topics": [
        "getDefaultFontFamily"
      ]
    },
    {
      "page": "getExpVarLabel",
      "title": "Helper function to print PC and explained variances",
      "topics": [
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      ]
    },
    {
      "page": "getLims",
      "title": "Get xlim/ylim ranges for plots from real values",
      "topics": [
        "getLims"
      ]
    },
    {
      "page": "ggSmoothScatter",
      "title": "Mimicking the graphics::smoothScatter behaviour for GGally::ggpairs",
      "topics": [
        "ggSmoothScatter"
      ]
    },
    {
      "page": "ggSmoothScatterWithAux",
      "title": "Mimicking the graphics::smoothScatter behaviour for GGally::ggpairs, with aux lines",
      "topics": [
        "ggSmoothScatterWithAux"
      ]
    },
    {
      "page": "guessWH",
      "title": "Guess width and height parameters for a heatmap",
      "topics": [
        "guessWH"
      ]
    },
    {
      "page": "histMat",
      "title": "Make histograms for matrix",
      "topics": [
        "histMat"
      ]
    },
    {
      "page": "idev",
      "title": "Interative dev.print and pdf print",
      "topics": [
        "idev",
        "ipdf"
      ]
    },
    {
      "page": "intRange",
      "title": "Return a range defined by integers",
      "topics": [
        "intRange"
      ]
    },
    {
      "page": "jitter.xyplot",
      "title": "Make boxplots or dotplots with sample-size proportional jitters",
      "topics": [
        "jitter.xyplot"
      ]
    },
    {
      "page": "midCol",
      "title": "Blender two colors to get the midpoint color of two colors",
      "topics": [
        "midCol"
      ]
    },
    {
      "page": "nonNull",
      "title": "Make sure that x is assigned a reasonable value",
      "topics": [
        "nonNull"
      ]
    },
    {
      "page": "openFileDevice",
      "title": "Open a device as a file preparing for plotting in the file",
      "topics": [
        "closeFileDevice",
        "openFileDevice"
      ]
    },
    {
      "page": "p2asterisk",
      "title": "Convert p values into asterisks",
      "topics": [
        "p2asterisk"
      ]
    },
    {
      "page": "panel.cor",
      "title": "Correlation panel for pairs",
      "topics": [
        "panel.cor"
      ]
    },
    {
      "page": "panel.lmSmooth",
      "title": "Correlation panel",
      "topics": [
        "panel.lmSmooth"
      ]
    },
    {
      "page": "pcaRotation",
      "title": "Retrieve PCA rotations from prcomp objects",
      "topics": [
        "pcaRotation"
      ]
    },
    {
      "page": "PCAScoreMatrix",
      "title": "Construct a S3-class PCAScoreMatrix object",
      "topics": [
        "PCAScoreMatrix"
      ]
    },
    {
      "page": "pcaScores",
      "title": "Retrieve PCA scores from prcomp objects",
      "topics": [
        "pcaScores"
      ]
    },
    {
      "page": "pcaScoresFromLogFC",
      "title": "Perform principal component analysis and derive PCA scores from a logFC matrix",
      "topics": [
        "pcaScoresFromLogFC"
      ]
    },
    {
      "page": "pdf2png",
      "title": "Use 'convert' (ImageMagick) to convert PDF to high-quality PNG",
      "topics": [
        "pdf2png"
      ]
    },
    {
      "page": "plotPCA",
      "title": "S3 method plotPCA",
      "topics": [
        "plotPCA"
      ]
    },
    {
      "page": "plotPCA.prcomp",
      "title": "Visualise PCA results of expression data with the sample plot",
      "topics": [
        "plotPCA.prcomp"
      ]
    },
    {
      "page": "plotPCAloading",
      "title": "Plot PCA loading",
      "topics": [
        "plotPCAloading"
      ]
    },
    {
      "page": "plotVenn",
      "title": "Plot Venn object of the Vennerable package",
      "topics": [
        "plotVenn"
      ]
    },
    {
      "page": "print.fcol",
      "title": "Print a fcol object",
      "topics": [
        "print.fcol"
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    },
    {
      "page": "print.PCAScoreMatrix",
      "title": "Print PCAScoreMatrix",
      "topics": [
        "print.PCAScoreMatrix"
      ]
    },
    {
      "page": "qBreaks",
      "title": "Internal function to re-calculate breaks of histograms when x-axis is clipped",
      "topics": [
        "qBreaks"
      ]
    },
    {
      "page": "qHist",
      "title": "Histogram with quantile line(s) and text(s)",
      "topics": [
        "qHist"
      ]
    },
    {
      "page": "radian2degree",
      "title": "Convert radian to degree values",
      "topics": [
        "radian2degree"
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    },
    {
      "page": "robustDist",
      "title": "Robust distance",
      "topics": [
        "robustDist"
      ]
    },
    {
      "page": "royalbluered",
      "title": "Two and three-color panels",
      "topics": [
        "blackgoldred",
        "blackgreen",
        "blackred",
        "blackredyellow",
        "blackwhite",
        "blackyellow",
        "blueblackred",
        "bluered",
        "cyanblackyellow",
        "greenred",
        "heat",
        "magentayellow",
        "redblackblue",
        "redblue",
        "redgreen",
        "royalbluegrayred",
        "royalbluered",
        "royalredblue",
        "royalredgrayblue",
        "turyeb",
        "whiteblack",
        "whiteblue",
        "whiteblueblackheat",
        "whitered",
        "yellowblack",
        "yellowblackcyan",
        "yellowmagenta"
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    },
    {
      "page": "setCompactTrellis",
      "title": "Set compact trellis as default",
      "topics": [
        "setCompactTrellis"
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    },
    {
      "page": "squareLayout",
      "title": "Plan a square/matrix layout of plots",
      "topics": [
        "squareLayout"
      ]
    },
    {
      "page": "symrange",
      "title": "Return a symmetric range",
      "topics": [
        "symrange"
      ]
    },
    {
      "page": "threecolor.panels",
      "title": "Return available three-color panels",
      "topics": [
        "threecolor.panels"
      ]
    },
    {
      "page": "twocolor.panels",
      "title": "Return available three-color panels",
      "topics": [
        "twocolor.panels"
      ]
    },
    {
      "page": "vennMembersDataframe",
      "title": "Extract members of each region in Venn diagrams in to a data.frame",
      "topics": [
        "vennMembersDataframe"
      ]
    },
    {
      "page": "vennMembersList",
      "title": "Extract members of each region in Venn diagrams in to a list",
      "topics": [
        "vennMembersList"
      ]
    },
    {
      "page": "xclipHist",
      "title": "Histogram with clipped x axis",
      "topics": [
        "xclipHist"
      ]
    }
  ],
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