RCircos: Circos 2D Track Plot

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.

AuthorHongen Zhang
Date of publication2016-09-28 07:21:49
MaintainerHongen Zhang <hzhang.henry@gmail.com>
LicenseGPL (>= 2)
Version1.2.0
http://bitbucket.org/henryhzhang/rcircos

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

Functions

RCircos Man page
RCircos.Adjust.Scatter.Values Man page
RCircos.Area.Highlight Man page
RCircos.Area.Plot Man page
RCircos.Chromosome.Ideogram.Plot Man page
RCircos.Clear.Track Man page
RCircos.Clear.Zoom.Area Man page
RCircos.Customized.Shape.Plot Man page
RCircos.Data.Point Man page
RCircos.defaultBasePerUnits Man page
RCircos.defaultCharWidth Man page
RCircos.defaultChromPadding Man page
RCircos.defaultCircosUnits Man page
RCircos.defaultTextSize Man page
RCircos.Draw.Chromosome.Ideogram Man page
RCircos.Env Man page
RCircos.Gene.Connector.Plot Man page
RCircos.Gene.Label.Data Man page
RCircos.Gene.Name.Plot Man page
RCircos.Get.Arrow.Shape Man page
RCircos.Get.Chromosome.Order Man page
RCircos.Get.Data.Point.Height Man page
RCircos.Get.Default.Base.Per.Units Man page
RCircos.Get.Default.Char.Width Man page
RCircos.Get.Default.Chrom.Padding Man page
RCircos.Get.Default.Circos.Units Man page
RCircos.Get.Default.Text.Size Man page
RCircos.Get.Gene.Label.Locations Man page
RCircos.Get.Gene.Name.Plot.Parameters Man page
RCircos.Get.Heatmap.Color.Scale Man page
RCircos.Get.Heatmap.Color.Scale.Location Man page
RCircos.Get.Heatmap.Data.Colors Man page
RCircos.Get.Link.Colors Man page
RCircos.Get.Padding.Constant Man page
RCircos.Get.Paired.Points.Positions Man page
RCircos.Get.Plot.Boundary Man page
RCircos.Get.Plot.Colors Man page
RCircos.Get.Plot.Ideogram Man page
RCircos.Get.Plot.Layers Man page
RCircos.Get.Plot.Parameters Man page
RCircos.Get.Plot.Positions Man page
RCircos.Get.Polygon.Height Man page
RCircos.Get.Single.Point.Positions Man page
RCircos.Get.Start.End.Locations Man page
RCircos.Get.Supported.HeatmapColors Man page
RCircos.Get.Supported.Plot.Types Man page
RCircos.Get.Track.Positions Man page
RCircos.Get.Zoom.Data Man page
RCircos.Get.Zoom.Range Man page
RCircos.heatmapColors Man page
RCircos.Heatmap.Data Man page
RCircos.Heatmap.Plot Man page
RCircos.Highligh.Chromosome.Ideogram Man page
RCircos.Histogram.Data Man page
RCircos.Histogram.Plot Man page
RCircos.Ideogram.Tick.Plot Man page
RCircos.Initialize.Plot.Parameters Man page
RCircos.Label.Chromosome.Names Man page
RCircos.Label.Zoom.Region Man page
RCircos.Line.Data Man page
RCircos.Line.Plot Man page
RCircos.Link.Data Man page
RCircos.Link.Line Man page
RCircos.Link.Plot Man page
RCircos.List.Plot.Parameters Man page
RCircos.Mark.Zoom.Area Man page
RCircos.Mouse.Expr.Data Man page
RCircos.Multiple.Species.Core.Components Man page
RCircos.Multiple.Species.Dataset Man page
RCircos-package Man page
RCircos.paddingConst Man page
RCircos.Parallel.Line.Plot Man page
RCircos.Plot.Heatmap.Color.Scale Man page
RCircos.plotTypes Man page
RCircos.Plot.Zoomed.Area Man page
RCircos.Plot.Zoomed.Continue.Lines Man page
RCircos.Plot.Zoomed.Gene.Connectors Man page
RCircos.Plot.Zoomed.Heatmap Man page
RCircos.Plot.Zoomed.Histogram Man page
RCircos.Plot.Zoomed.Ideogram.Ticks Man page
RCircos.Plot.Zoomed.Parallel.Lines Man page
RCircos.Plot.Zoomed.Polygons Man page
RCircos.Plot.Zoomed.Scatters Man page
RCircos.Plot.Zoomed.Tiles Man page
RCircos.Plot.Zoomed.Vertical.Lines Man page
RCircos.Point.Plot Man page
RCircos.Polygon.Data Man page
RCircos.Polygon.Plot Man page
RCircos.Pseudo.Ideogram.From.Labels Man page
RCircos.Pseudo.Ideogram.From.Table Man page
RCircos.Rat.Expr.Data Man page
RCircos.Ribbon.Data Man page
RCircos.Ribbon.Plot Man page
RCircos.Scatter.Data Man page
RCircos.Scatter.Plot Man page
RCircos.Set.Base.Plot.Positions Man page
RCircos.Set.Core.Components Man page
RCircos.Set.Cytoband.Data Man page
RCircos.Set.Plot.Area Man page
RCircos.Set.Zoom.Plot.Positions Man page
RCircos.Sort.Genomic.Data Man page
RCircos.Tile.Data Man page
RCircos.Tile.Plot Man page
RCircos.Track.Outline Man page
RCircos.Validate.Cyto.Info Man page
RCircos.Validate.Genomic.Data Man page
RCircos.Validate.Genomic.Info Man page
RCircos.Validate.Plot.Parameters Man page
RCircos.Validate.Track.Positions Man page
RCircos.Vertical.Line.Plot Man page
RCircos.Workflow Man page
RCircos.Zoom.Area.Outline Man page
RCircos.ZoomIn.Chromosome Man page
RCircos.ZoomOut.Chromosome Man page
RCircos.Zoom.Paired.Plot.Positions Man page
RCircos.Zoom.Single.Plot.Positions Man page
UCSC.Baylor.3.4.Rat.cytoBandIdeogram Man page
UCSC.HG19.Human.CytoBandIdeogram Man page
UCSC.HG38.Human.CytoBandIdeogram Man page
UCSC.Mouse.GRCm38.CytoBandIdeogram Man page

Files

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

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