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.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.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 |