# Circos 2D Track Plot

## Documentation for package ‘RCircos’ version 1.2.0

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

## Help Pages

R U misc

RCircos-package | Circos-like Plot of Genomic Data

## -- R --

RCircos | Circos-like Plot of Genomic Data
RCircos.Adjust.Scatter.Values | Adjust Scatter Plot Data to Fit the Data Track
RCircos.Area.Highlight | Highlight PLot Area Cross One or More Tracks
RCircos.Area.Plot | Paint Areas on One Data Track
RCircos.Chromosome.Ideogram.Plot | Plot Chromosome Ideogram
RCircos.Clear.Track | Erase One or More Data Tracks
RCircos.Clear.Zoom.Area | Erase Zoom-in Plot Area
RCircos.Customized.Shape.Plot | Plot A Customized Shape
RCircos.Data.Point | Convert A Genomic Position to An Index of Circos Plot Position
RCircos.defaultBasePerUnits | The Default Base Pair Number of A Circos Unit
RCircos.defaultCharWidth | Default Character With in Circos Unit
RCircos.defaultChromPadding | The Default Value of GAP in Circos (Chromosome) Unit between two Chromosome Ideogram
RCircos.defaultCircosUnits | Default Circos Units for RCircos
RCircos.defaultTextSize | Default Character Size of RCircos Plot
RCircos.Draw.Chromosome.Ideogram | Plot Chromosome Ideogram
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.Arrow.Shape | Get Default Coordinates for An Arrow Shape
RCircos.Get.Chromosome.Order | Find the order of Chromosome Names
RCircos.Get.Data.Point.Height | Calculate the Height of Data in A Track
RCircos.Get.Default.Base.Per.Units | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Default.Char.Width | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Default.Chrom.Padding | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Default.Circos.Units | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Default.Text.Size | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Gene.Label.Locations | Calculate Plot Positions for Gene Labels
RCircos.Get.Gene.Name.Plot.Parameters | Calculate Parameters for Gene Name Plot
RCircos.Get.Heatmap.Color.Scale | Generate Color Scales for Heatmap Plot
RCircos.Get.Heatmap.Color.Scale.Location | Calculate X and Y Coordinates for Color Scale
RCircos.Get.Heatmap.Data.Colors | Set Colors for One Track of Heatmap
RCircos.Get.Link.Colors | Set up Colors for Link Lines or Ribbons
RCircos.Get.Padding.Constant | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Paired.Points.Positions | Calcualte Plot Positions for A Genomic Interval
RCircos.Get.Plot.Boundary | Calculate Boundary of A Data Track
RCircos.Get.Plot.Colors | Assign Plot Colors for Non-Link Data Plot
RCircos.Get.Plot.Ideogram | Methods to Retrieve RCircos Core Components Used in Current RCircos Session
RCircos.Get.Plot.Layers | Get the Layer Numbers for Tile Plot
RCircos.Get.Plot.Parameters | Methods to Retrieve RCircos Core Components Used in Current RCircos Session
RCircos.Get.Plot.Positions | Methods to Retrieve RCircos Core Components Used in Current RCircos Session
RCircos.Get.Polygon.Height | Calculate the Height of Polygons in A Data Track
RCircos.Get.Single.Point.Positions | Calculate Plot Positions for Genomic Data
RCircos.Get.Start.End.Locations | Calculate Start and End Positions for Plot Data
RCircos.Get.Supported.HeatmapColors | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Supported.Plot.Types | Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Track.Positions | Calculate Plot Positions for A Data Track
RCircos.Get.Zoom.Data | Retriev Subset of Plot Data for Zoom
RCircos.Get.Zoom.Range | Retrieve Genomic Interval from Genomic Data for Zoom Plot
RCircos.Heatmap.Data | Sample Data for RCircos Heatmap Plot
RCircos.Heatmap.Plot | Draw Heatmap for One Data Track
RCircos.heatmapColors | Heatmap Colors Supported by Current Version of RCircos
RCircos.Highligh.Chromosome.Ideogram | Plot Chromosome Ideogram
RCircos.Histogram.Data | Sample Data for RCircos Histogram Plot
RCircos.Histogram.Plot | Plot Histogram for One Data Track
RCircos.Ideogram.Tick.Plot | Plot Chromosome Ideogram
RCircos.Initialize.Plot.Parameters | Initialize RCircos Plot Parameters
RCircos.Label.Chromosome.Names | Plot Chromosome Ideogram
RCircos.Label.Zoom.Region | Zoomed-in Plot of Small Genomic Region
RCircos.Line.Data | Sample Data for RCircos Line Plot
RCircos.Line.Plot | Draw Lines for One Data Track
RCircos.Link.Data | Sample Data for RCircos Link Plot
RCircos.Link.Line | Calculate x and y Coordinates for a Bezire Curve
RCircos.Link.Plot | Draw Link Lines between Two or More Genomic Positions
RCircos.List.Plot.Parameters | List RCircos Plot Parameters
RCircos.Mark.Zoom.Area | Zoomed-in Plot of Small Genomic Region
RCircos.Mouse.Expr.Data | Sample Data of Mouse Gene Expression
RCircos.Multiple.Species.Core.Components | Setup RCircos Core Components with Multiple Species Genomes
RCircos.Multiple.Species.Dataset | Combine Multiple Data Sets form Different Genomes
RCircos.paddingConst | Padding Distance Constant between Two Chromosomes
RCircos.Parallel.Line.Plot | Draw Lines between Two Genomic Positions on Same Chromosome
RCircos.Plot.Heatmap.Color.Scale | Plot A Color Scale for Heatmap
RCircos.Plot.Zoomed.Area | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Continue.Lines | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Gene.Connectors | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Heatmap | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Histogram | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Ideogram.Ticks | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Parallel.Lines | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Polygons | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Scatters | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Tiles | Zoomed-in Plot of Small Genomic Region
RCircos.Plot.Zoomed.Vertical.Lines | Zoomed-in Plot of Small Genomic Region
RCircos.plotTypes | Plot Types Supported by Current RCircos Version
RCircos.Point.Plot | Point Plot for One Data Track
RCircos.Polygon.Data | RCircos Polygon Demo Data
RCircos.Polygon.Plot | Draw Polygons on One Data Track
RCircos.Pseudo.Ideogram.From.Labels | Generate A Pseudo Chromosome Ideogram from List of Lables
RCircos.Pseudo.Ideogram.From.Table | Generate Pseudo Chromosome Ideogram from Plot Data Table
RCircos.Rat.Expr.Data | Sample Data of Rat Gene Expression
RCircos.Reset.Plot.Ideogram | Reset Methods for Modifying RCircos Core Components
RCircos.Reset.Plot.Parameters | Reset Methods for Modifying RCircos Core Components
RCircos.Reset.Plot.Positions | Reset Methods for Modifying RCircos Core Components
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 | Scater Plot for One Data Track
RCircos.Set.Base.Plot.Positions | Setup Base Plot Positions
RCircos.Set.Core.Components | Initialize Core Components for RCircos Plot
RCircos.Set.Cytoband.Data | Set Chromosome Cytoband Data for Circos Plot
RCircos.Set.Plot.Area | Setup Plot Area for RCircos Plot
RCircos.Set.Zoom.Plot.Positions | Set Position for Zoom-in Plot
RCircos.Sort.Genomic.Data | Sort Genomic or Ideogram Data
RCircos.Tile.Data | Sample Data for RCircos Tile Plot
RCircos.Tile.Plot | Plot Tiles for One Data Track
RCircos.Track.Outline | Draw Outline for A Data Track
RCircos.Validate.Cyto.Info | Validate Chromosome Ideogram Information
RCircos.Validate.Genomic.Data | Validate Genomic Data
RCircos.Validate.Genomic.Info | Validate Genomic Information
RCircos.Validate.Plot.Parameters | Validate Plot Parameters
RCircos.Validate.Track.Positions | Validate Track Positions
RCircos.Vertical.Line.Plot | Draw Vertical Lines on One Data Track
RCircos.Workflow | A Simple RCircos Plot Workflow
RCircos.Zoom.Area.Outline | Draw Outline for Zoom Plot Area
RCircos.Zoom.Paired.Plot.Positions | Calculate Zoomed Index of Circos Plot Positions for Genomic Intervals
RCircos.Zoom.Single.Plot.Positions | Calculate Zoomed Index of Circos Plot Positions for Single Point Genomic Data
RCircos.ZoomIn.Chromosome | Zoom in One or Partial Chromosome Ideogram
RCircos.ZoomOut.Chromosome | Zoom out Chromosome Ideogram

## -- U --

UCSC.Baylor.3.4.Rat.cytoBandIdeogram | Cytoband Information for Rat Chromosome Ideogram
UCSC.HG19.Human.CytoBandIdeogram | Cytoband Information for Human Chromosome Ideogram
UCSC.HG38.Human.CytoBandIdeogram | Human Chromosome Ideogram Version 38
UCSC.Mouse.GRCm38.CytoBandIdeogram | Cytoband Inforamtion for Mouse Chromosome Ideogram

## -- misc --

| Reset Methods for Modifying RCircos Core Components