# Circos 2D Track Plot

## Documentation for package ‘RCircos’ version 1.1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

RCircos-package | Circos-like Plot of Genomic Data
RCircos | Circos-like Plot of Genomic Data
RCircos.Add.Ideogram.Tick | Add Ticks onto Chromosome Ideogram
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.Reset.Plot.Positions | Reset RCircos Base Position
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