Circos 2D Track Plot

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Documentation for package ‘RCircos’ version 1.1.2

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RCircos-package Circos-like Plot of Genomic Data
RCircos Circos-like Plot of Genomic Data
RCircos.Chromosome.Ideogram.Plot Draw Chromosome Ideogram
RCircos.Clear.Track Erase One or More Data Tracks
RCircos.Data.Point Convert a Genomic Position to an Index of Circos Plot Position
RCircos.Env RCircos Environment
RCircos.Gene.Connector.Plot Draw Connectors between Chromosome Ideogram and Gene Names
RCircos.Gene.Label.Data Sample Data for Gene Labels
RCircos.Gene.Name.Plot Draw Gene Names on a Data Track
RCircos.Get.Gene.Label.Locations Calculate New Position for Gene Labels
RCircos.Get.Heatmap.ColorScales Generate Color Scales for Heatmap Plot
RCircos.Get.Link.Colors Set up Colors for Link Lines or Ribbons
RCircos.Get.Plot.Colors Assign Plot Colors for Non-Link Data Plot
RCircos.Get.Plot.Data Convert Genomic Data to RCircos Plot Data
RCircos.Get.Plot.Ideogram Get Chromosome Ideogram Object
RCircos.Get.Plot.Parameters Get All RCircos Plot Parameters
RCircos.Get.Plot.Positions Get RCircos Plot Position Object
RCircos.Heatmap.Data Sample Data for RCircos Heatmap Plot
RCircos.Heatmap.Plot Circos-like Heamap Plot
RCircos.Histogram.Data Sample Data for RCircos Histogram Plot
RCircos.Histogram.Plot Circos-like Histogram Plot
RCircos.Initialize.Parameters Initialize RCircos Plot Parameters
RCircos.Line.Data Sample Data for RCircos Line Plot
RCircos.Line.Plot Circos-like Line Plot
RCircos.Link.Data Sample Data for RCircos Link Plot
RCircos.Link.Line Calculate x and y Coordinates for a Bezire Curve
RCircos.Link.Plot Circos-like Link Line Plot
RCircos.List.Parameters Print RCircos Parameters to Standard Output
RCircos.Mouse.Expr.Data Sample Data of Mouse Gene Expression
RCircos.Multiple.Species.Core.Components Setup RCircos Core Components with Multiple Species
RCircos.Multiple.Species.Dataset Construct A Dataset from Multiple Genomic Data of Different Species
RCircos.Rat.Expr.Data Sample Data of Rat Gene Expression
RCircos.Reset.Plot.Ideogram Reset RCircos Ideogram Plot Data
RCircos.Reset.Plot.Parameters Reset RCircos Plot Parameters
RCircos.Ribbon.Data Sample Data for RCircos Ribbon Plot
RCircos.Ribbon.Plot Draw Ribbon between Two Genomic Regions
RCircos.Scatter.Data Sample Data for RCircos Scatter Plot
RCircos.Scatter.Plot Circos-like Scatter Plot
RCircos.Set.Base.Plot.Positions Setup Base Plot Positions
RCircos.Set.Core.Components Initialize Core Components for RCircos Plot
RCircos.Set.Cytoband.data Setup Chromosome Cytoband Data for RCircos Plot
RCircos.Set.Plot.Area Setup Plot Area for RCircos Plot
RCircos.Tile.Data Sample Data for RCircos Tile Plot
RCircos.Tile.Plot Circos-like Tile Plot
RCircos.Track.Outline Draw Outline for A Data Plot Track
RCircos.Track.Positions Calculate Data Plot Track Positions
RCircos.Validate.Cyto.Info Validate Chromosome Ideogram Data
RCircos.Validate.Genomic.Data Validate Genomic Data for RCircos Plot
RCircos.Workflow Print Out RCircos Workflow
UCSC.Baylor.3.4.Rat.cytoBandIdeogram Cytoband Information for Rat Chromosome Ideogram
UCSC.HG19.Human.CytoBandIdeogram Cytoband Information for Human Chromosome Ideogram
UCSC.Mouse.GRCm38.CytoBandIdeogram Cytoband Inforamtion for Mouse Chromosome Ideogram