RCircos: Circos 2D Track Plot

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A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

Author
Hongen Zhang
Date of publication
2016-09-28 07:21:49
Maintainer
Hongen Zhang <hzhang.henry@gmail.com>
License
GPL (>= 2)
Version
1.2.0
URLs

View on CRAN

Man pages

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...
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...
RCircos.defaultCircosUnits
Default Circos Units for RCircos
RCircos.defaultTextSize
Default Character Size of RCircos Plot
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.Core.Components
Methods to Retrieve RCircos Core Components Used in Current...
RCircos.Get.Data.Point.Height
Calculate the Height of Data in A Track
RCircos.Get.Default.Parameters
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.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.heatmapColors
Heatmap Colors Supported by Current Version of RCircos
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-package
Circos-like Plot of Genomic Data
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.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.Core.Components
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.ZoomIn.Chromosome
Zoom in One or Partial Chromosome Ideogram
RCircos.ZoomIn.Plot
Zoomed-in Plot of Small Genomic Region
RCircos.ZoomOut.Chromosome
Zoom out Chromosome Ideogram
RCircos.Zoom.Paired.Plot.Positions
Calculate Zoomed Index of Circos Plot Positions for Genomic...
RCircos.Zoom.Single.Plot.Positions
Calculate Zoomed Index of Circos Plot Positions for Single...
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

Files in this package

RCircos
RCircos/inst
RCircos/inst/CITATION
RCircos/inst/doc
RCircos/inst/doc/RCircos-manual.pdf
RCircos/inst/doc/Using_RCircos.Rnw
RCircos/inst/doc/Using_RCircos.pdf
RCircos/inst/doc/Using_RCircos.R
RCircos/NAMESPACE
RCircos/demo
RCircos/demo/RCircos.Ribbon.Plot.Demo.R
RCircos/demo/RCircos.Layout.Demo.R
RCircos/demo/RCircos.Heatmap.Demo.R
RCircos/demo/RCircos.Polygon.Plot.Demo.R
RCircos/demo/RCircos.Chromosome.Tick.Demo.R
RCircos/demo/RCircos.Gene.Connector.Demo.R
RCircos/demo/RCircos.Histogram.Demo.R
RCircos/demo/RCircos.Demo.Human.R
RCircos/demo/RCircos.Line.Plot.Demo.R
RCircos/demo/RCircos.Zoom.Plot.Demo.R
RCircos/demo/RCircos.Tile.Plot.Demo.R
RCircos/demo/RCircos.Area.Plot.Demo.R
RCircos/demo/RCircos.Link.Plot.Demo.R
RCircos/demo/00Index
RCircos/demo/RCircos.Demo.Mouse.And.Rat.R
RCircos/demo/RCircos.Scatter.Plot.Demo.R
RCircos/data
RCircos/data/UCSC.Mouse.GRCm38.CytoBandIdeogram.RData
RCircos/data/RCircos.Tile.Data.RData
RCircos/data/RCircos.Scatter.Data.RData
RCircos/data/RCircos.Ribbon.Data.RData
RCircos/data/UCSC.HG38.Human.CytoBandIdeogram.RData
RCircos/data/UCSC.Baylor.3.4.Rat.cytoBandIdeogram.RData
RCircos/data/RCircos.Heatmap.Data.RData
RCircos/data/RCircos.Histogram.Data.RData
RCircos/data/UCSC.HG19.Human.CytoBandIdeogram.RData
RCircos/data/RCircos.Polygon.Data.RData
RCircos/data/RCircos.Line.Data.RData
RCircos/data/RCircos.Link.Data.RData
RCircos/data/RCircos.Mouse.Expr.Data.RData
RCircos/data/RCircos.Gene.Label.Data.RData
RCircos/data/RCircos.Rat.Expr.Data.RData
RCircos/R
RCircos/R/RCircosZoomPlot.R
RCircos/R/RCircosPlotPositions.R
RCircos/R/RCircosGenomicData.R
RCircos/R/RCircosPlotParameters.R
RCircos/R/RCircosChromosomeIdeogram.R
RCircos/R/RCircosMain.R
RCircos/R/RCircosHeatmap.R
RCircos/R/RCircosPlotDataTracks.R
RCircos/vignettes
RCircos/vignettes/RCircosDemoHuman.png
RCircos/vignettes/RCircosLayoutDemo.png
RCircos/vignettes/Using_RCircos.Rnw
RCircos/MD5
RCircos/build
RCircos/build/vignette.rds
RCircos/DESCRIPTION
RCircos/man
RCircos/man/RCircos.Line.Plot.Rd
RCircos/man/RCircos.Validate.Genomic.Data.Rd
RCircos/man/RCircos.defaultCharWidth.Rd
RCircos/man/RCircos.Customized.Shape.Plot.Rd
RCircos/man/RCircos.Get.Plot.Colors.Rd
RCircos/man/RCircos.ZoomIn.Plot.Rd
RCircos/man/RCircos.Zoom.Area.Outline.Rd
RCircos/man/RCircos.Scatter.Plot.Rd
RCircos/man/RCircos.Validate.Track.Positions.Rd
RCircos/man/RCircos.Get.Heatmap.Data.Colors.Rd
RCircos/man/RCircos.Get.Core.Components.Rd
RCircos/man/RCircos.Set.Plot.Area.Rd
RCircos/man/RCircos.Initialize.Plot.Parameters.Rd
RCircos/man/RCircos.Tile.Plot.Rd
RCircos/man/RCircos.Validate.Cyto.Info.Rd
RCircos/man/UCSC.HG38.Human.CytoBandIdeogram.Rd
RCircos/man/RCircos.Link.Line.Rd
RCircos/man/RCircos.ZoomIn.Chromosome.Rd
RCircos/man/RCircos.Zoom.Paired.Plot.Positions.Rd
RCircos/man/RCircos.Gene.Name.Plot.Rd
RCircos/man/RCircos.Ribbon.Plot.Rd
RCircos/man/RCircos.Get.Heatmap.Color.Scale.Location.Rd
RCircos/man/RCircos.Heatmap.Plot.Rd
RCircos/man/RCircos.Parallel.Line.Plot.Rd
RCircos/man/RCircos.plotTypes.Rd
RCircos/man/RCircos.Polygon.Data.Rd
RCircos/man/RCircos.Get.Zoom.Data.Rd
RCircos/man/RCircos.Workflow.Rd
RCircos/man/RCircos.Get.Gene.Name.Plot.Parameters.Rd
RCircos/man/RCircos.Heatmap.Data.Rd
RCircos/man/RCircos.Pseudo.Ideogram.From.Table.Rd
RCircos/man/RCircos.Get.Arrow.Shape.Rd
RCircos/man/RCircos.defaultCircosUnits.Rd
RCircos/man/RCircos.Rat.Expr.Data.Rd
RCircos/man/RCircos.Area.Plot.Rd
RCircos/man/RCircos.Link.Data.Rd
RCircos/man/RCircos.Get.Gene.Label.Locations.Rd
RCircos/man/RCircos.Get.Zoom.Range.Rd
RCircos/man/RCircos.Line.Data.Rd
RCircos/man/RCircos.Get.Plot.Boundary.Rd
RCircos/man/RCircos.Get.Single.Point.Positions.Rd
RCircos/man/RCircos.Validate.Plot.Parameters.Rd
RCircos/man/RCircos.Pseudo.Ideogram.From.Labels.Rd
RCircos/man/RCircos.Link.Plot.Rd
RCircos/man/RCircos.Get.Start.End.Locations.Rd
RCircos/man/RCircos.Validate.Genomic.Info.Rd
RCircos/man/RCircos.Mouse.Expr.Data.Rd
RCircos/man/RCircos.Get.Plot.Layers.Rd
RCircos/man/RCircos.Ribbon.Data.Rd
RCircos/man/UCSC.Baylor.3.4.Rat.cytoBandIdeogram.Rd
RCircos/man/RCircos.Get.Paired.Points.Positions.Rd
RCircos/man/RCircos.Histogram.Plot.Rd
RCircos/man/RCircos.Get.Polygon.Height.Rd
RCircos/man/RCircos.Gene.Connector.Plot.Rd
RCircos/man/RCircos.Get.Track.Positions.Rd
RCircos/man/RCircos.Multiple.Species.Core.Components.Rd
RCircos/man/RCircos.defaultTextSize.Rd
RCircos/man/UCSC.HG19.Human.CytoBandIdeogram.Rd
RCircos/man/RCircos.Get.Default.Parameters.Rd
RCircos/man/RCircos.Plot.Heatmap.Color.Scale.Rd
RCircos/man/RCircos.Env.Rd
RCircos/man/RCircos.Get.Link.Colors.Rd
RCircos/man/RCircos.Scatter.Data.Rd
RCircos/man/RCircos.Gene.Label.Data.Rd
RCircos/man/RCircos.Clear.Track.Rd
RCircos/man/RCircos.defaultChromPadding.Rd
RCircos/man/RCircos.paddingConst.Rd
RCircos/man/RCircos.defaultBasePerUnits.Rd
RCircos/man/RCircos.Sort.Genomic.Data.Rd
RCircos/man/RCircos.Area.Highlight.Rd
RCircos/man/RCircos.Get.Chromosome.Order.Rd
RCircos/man/RCircos.Track.Outline.Rd
RCircos/man/RCircos.Get.Heatmap.Color.Scale.Rd
RCircos/man/RCircos-package.Rd
RCircos/man/RCircos.Set.Cytoband.Data.Rd
RCircos/man/RCircos.List.Plot.Parameters.Rd
RCircos/man/RCircos.Tile.Data.Rd
RCircos/man/RCircos.ZoomOut.Chromosome.Rd
RCircos/man/RCircos.Clear.Zoom.Area.Rd
RCircos/man/RCircos.Set.Base.Plot.Positions.Rd
RCircos/man/RCircos.Chromosome.Ideogram.Plot.Rd
RCircos/man/RCircos.Vertical.Line.Plot.Rd
RCircos/man/UCSC.Mouse.GRCm38.CytoBandIdeogram.Rd
RCircos/man/RCircos.Histogram.Data.Rd
RCircos/man/RCircos.Set.Core.Components.Rd
RCircos/man/RCircos.Multiple.Species.Dataset.Rd
RCircos/man/RCircos.Polygon.Plot.Rd
RCircos/man/RCircos.Reset.Core.Components.Rd
RCircos/man/RCircos.heatmapColors.Rd
RCircos/man/RCircos.Point.Plot.Rd
RCircos/man/RCircos.Zoom.Single.Plot.Positions.Rd
RCircos/man/RCircos.Adjust.Scatter.Values.Rd
RCircos/man/RCircos.Set.Zoom.Plot.Positions.Rd
RCircos/man/RCircos.Get.Data.Point.Height.Rd
RCircos/man/RCircos.Data.Point.Rd