Package index • RCircos

All functions

RCircos-package 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() RCircos.Draw.Chromosome.Ideogram() RCircos.Highligh.Chromosome.Ideogram() RCircos.Ideogram.Tick.Plot() RCircos.Label.Chromosome.Names(): Plot Chromosome Ideogram

RCircos.Clear.Track(): Erase One or More Data Tracks

RCircos.Clear.Zoom.Area(): Erase Zoom-in Plot Area

RCircos.Customized.Connection.Plot(): Draw Connectors between Chromosome Ideogram and Gene Names

RCircos.Customized.Shape.Plot(): Plot A Customized Shape

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.Arrow.Shape(): Get Default Coordinates for An Arrow Shape

RCircos.Get.Chromosome.Order(): Find the order of Chromosome Names

RCircos.Get.Plot.Parameters() RCircos.Get.Plot.Positions() RCircos.Get.Plot.Ideogram(): Methods to Retrieve RCircos Core Components Used in Current RCircos Session

RCircos.Get.Data.Point.Height(): Calculate the Height of Data in A Track

RCircos.Get.Default.Circos.Units() RCircos.Get.Default.Base.Per.Units() RCircos.Get.Default.Chrom.Padding() RCircos.Get.Padding.Constant() RCircos.Get.Supported.HeatmapColors() RCircos.Get.Supported.Plot.Types() RCircos.Get.Default.Char.Width() 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.Location(): Calculate X and Y Coordinates for Color Scale

RCircos.Get.Heatmap.Color.Scale(): Generate Color Scales for Heatmap Plot

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.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.Layers(): Get the Layer Numbers for Tile Plot

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.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.Histogram.Data: Sample Data for RCircos Histogram Plot

RCircos.Histogram.Plot(): Plot Histogram for One Data Track

RCircos.Initialize.Plot.Parameters(): Initialize RCircos Plot Parameters

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.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.Parallel.Line.Plot(): Draw Lines between Two Genomic Positions on Same Chromosome

RCircos.Plot.Heatmap.Color.Scale(): Plot A Color Scale for Heatmap

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() RCircos.Reset.Plot.Positions() RCircos.Reset.Plot.Parameters(): 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.Plot.Zoomed.Area() RCircos.Plot.Zoomed.Gene.Connectors() RCircos.Plot.Zoomed.Heatmap() RCircos.Plot.Zoomed.Histogram() RCircos.Plot.Zoomed.Ideogram.Ticks() RCircos.Plot.Zoomed.Continue.Lines() RCircos.Plot.Zoomed.Parallel.Lines() RCircos.Plot.Zoomed.Vertical.Lines() RCircos.Plot.Zoomed.Scatters() RCircos.Plot.Zoomed.Tiles() RCircos.Plot.Zoomed.Polygons() RCircos.Label.Zoom.Region() RCircos.Mark.Zoom.Area(): Zoomed-in Plot of Small Genomic Region

RCircos.ZoomOut.Chromosome(): Zoom out Chromosome Ideogram

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.heatmapColors: Heatmap Colors Supported by Current Version of RCircos

RCircos.paddingConst: Padding Distance Constant between Two Chromosomes

RCircos.plotTypes: Plot Types Supported by Current RCircos Version

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