RCircos: Circos 2D Track Plot
Version 1.2.0

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
URL http://bitbucket.org/henryhzhang/rcircos
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RCircos")

Getting started

Package overview

Popular man pages

RCircos.Chromosome.Ideogram.Plot: Plot Chromosome Ideogram
RCircos.Get.Link.Colors: Set up Colors for Link Lines or Ribbons
RCircos.Heatmap.Data: Sample Data for RCircos Heatmap Plot
RCircos.Link.Data: Sample Data for RCircos Link Plot
RCircos.Link.Plot: Draw Link Lines between Two or More Genomic Positions
RCircos-package: Circos-like Plot of Genomic Data
RCircos.Validate.Genomic.Data: Validate Genomic Data
See all...

All man pages Function index File listing

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

Files

inst
inst/CITATION
inst/doc
inst/doc/RCircos-manual.pdf
inst/doc/Using_RCircos.Rnw
inst/doc/Using_RCircos.pdf
inst/doc/Using_RCircos.R
NAMESPACE
demo
demo/RCircos.Ribbon.Plot.Demo.R
demo/RCircos.Layout.Demo.R
demo/RCircos.Heatmap.Demo.R
demo/RCircos.Polygon.Plot.Demo.R
demo/RCircos.Chromosome.Tick.Demo.R
demo/RCircos.Gene.Connector.Demo.R
demo/RCircos.Histogram.Demo.R
demo/RCircos.Demo.Human.R
demo/RCircos.Line.Plot.Demo.R
demo/RCircos.Zoom.Plot.Demo.R
demo/RCircos.Tile.Plot.Demo.R
demo/RCircos.Area.Plot.Demo.R
demo/RCircos.Link.Plot.Demo.R
demo/00Index
demo/RCircos.Demo.Mouse.And.Rat.R
demo/RCircos.Scatter.Plot.Demo.R
data
data/UCSC.Mouse.GRCm38.CytoBandIdeogram.RData
data/RCircos.Tile.Data.RData
data/RCircos.Scatter.Data.RData
data/RCircos.Ribbon.Data.RData
data/UCSC.HG38.Human.CytoBandIdeogram.RData
data/UCSC.Baylor.3.4.Rat.cytoBandIdeogram.RData
data/RCircos.Heatmap.Data.RData
data/RCircos.Histogram.Data.RData
data/UCSC.HG19.Human.CytoBandIdeogram.RData
data/RCircos.Polygon.Data.RData
data/RCircos.Line.Data.RData
data/RCircos.Link.Data.RData
data/RCircos.Mouse.Expr.Data.RData
data/RCircos.Gene.Label.Data.RData
data/RCircos.Rat.Expr.Data.RData
R
R/RCircosZoomPlot.R
R/RCircosPlotPositions.R
R/RCircosGenomicData.R
R/RCircosPlotParameters.R
R/RCircosChromosomeIdeogram.R
R/RCircosMain.R
R/RCircosHeatmap.R
R/RCircosPlotDataTracks.R
vignettes
vignettes/RCircosDemoHuman.png
vignettes/RCircosLayoutDemo.png
vignettes/Using_RCircos.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/RCircos.Line.Plot.Rd
man/RCircos.Validate.Genomic.Data.Rd
man/RCircos.defaultCharWidth.Rd
man/RCircos.Customized.Shape.Plot.Rd
man/RCircos.Get.Plot.Colors.Rd
man/RCircos.ZoomIn.Plot.Rd
man/RCircos.Zoom.Area.Outline.Rd
man/RCircos.Scatter.Plot.Rd
man/RCircos.Validate.Track.Positions.Rd
man/RCircos.Get.Heatmap.Data.Colors.Rd
man/RCircos.Get.Core.Components.Rd
man/RCircos.Set.Plot.Area.Rd
man/RCircos.Initialize.Plot.Parameters.Rd
man/RCircos.Tile.Plot.Rd
man/RCircos.Validate.Cyto.Info.Rd
man/UCSC.HG38.Human.CytoBandIdeogram.Rd
man/RCircos.Link.Line.Rd
man/RCircos.ZoomIn.Chromosome.Rd
man/RCircos.Zoom.Paired.Plot.Positions.Rd
man/RCircos.Gene.Name.Plot.Rd
man/RCircos.Ribbon.Plot.Rd
man/RCircos.Get.Heatmap.Color.Scale.Location.Rd
man/RCircos.Heatmap.Plot.Rd
man/RCircos.Parallel.Line.Plot.Rd
man/RCircos.plotTypes.Rd
man/RCircos.Polygon.Data.Rd
man/RCircos.Get.Zoom.Data.Rd
man/RCircos.Workflow.Rd
man/RCircos.Get.Gene.Name.Plot.Parameters.Rd
man/RCircos.Heatmap.Data.Rd
man/RCircos.Pseudo.Ideogram.From.Table.Rd
man/RCircos.Get.Arrow.Shape.Rd
man/RCircos.defaultCircosUnits.Rd
man/RCircos.Rat.Expr.Data.Rd
man/RCircos.Area.Plot.Rd
man/RCircos.Link.Data.Rd
man/RCircos.Get.Gene.Label.Locations.Rd
man/RCircos.Get.Zoom.Range.Rd
man/RCircos.Line.Data.Rd
man/RCircos.Get.Plot.Boundary.Rd
man/RCircos.Get.Single.Point.Positions.Rd
man/RCircos.Validate.Plot.Parameters.Rd
man/RCircos.Pseudo.Ideogram.From.Labels.Rd
man/RCircos.Link.Plot.Rd
man/RCircos.Get.Start.End.Locations.Rd
man/RCircos.Validate.Genomic.Info.Rd
man/RCircos.Mouse.Expr.Data.Rd
man/RCircos.Get.Plot.Layers.Rd
man/RCircos.Ribbon.Data.Rd
man/UCSC.Baylor.3.4.Rat.cytoBandIdeogram.Rd
man/RCircos.Get.Paired.Points.Positions.Rd
man/RCircos.Histogram.Plot.Rd
man/RCircos.Get.Polygon.Height.Rd
man/RCircos.Gene.Connector.Plot.Rd
man/RCircos.Get.Track.Positions.Rd
man/RCircos.Multiple.Species.Core.Components.Rd
man/RCircos.defaultTextSize.Rd
man/UCSC.HG19.Human.CytoBandIdeogram.Rd
man/RCircos.Get.Default.Parameters.Rd
man/RCircos.Plot.Heatmap.Color.Scale.Rd
man/RCircos.Env.Rd
man/RCircos.Get.Link.Colors.Rd
man/RCircos.Scatter.Data.Rd
man/RCircos.Gene.Label.Data.Rd
man/RCircos.Clear.Track.Rd
man/RCircos.defaultChromPadding.Rd
man/RCircos.paddingConst.Rd
man/RCircos.defaultBasePerUnits.Rd
man/RCircos.Sort.Genomic.Data.Rd
man/RCircos.Area.Highlight.Rd
man/RCircos.Get.Chromosome.Order.Rd
man/RCircos.Track.Outline.Rd
man/RCircos.Get.Heatmap.Color.Scale.Rd
man/RCircos-package.Rd
man/RCircos.Set.Cytoband.Data.Rd
man/RCircos.List.Plot.Parameters.Rd
man/RCircos.Tile.Data.Rd
man/RCircos.ZoomOut.Chromosome.Rd
man/RCircos.Clear.Zoom.Area.Rd
man/RCircos.Set.Base.Plot.Positions.Rd
man/RCircos.Chromosome.Ideogram.Plot.Rd
man/RCircos.Vertical.Line.Plot.Rd
man/UCSC.Mouse.GRCm38.CytoBandIdeogram.Rd
man/RCircos.Histogram.Data.Rd
man/RCircos.Set.Core.Components.Rd
man/RCircos.Multiple.Species.Dataset.Rd
man/RCircos.Polygon.Plot.Rd
man/RCircos.Reset.Core.Components.Rd
man/RCircos.heatmapColors.Rd
man/RCircos.Point.Plot.Rd
man/RCircos.Zoom.Single.Plot.Positions.Rd
man/RCircos.Adjust.Scatter.Values.Rd
man/RCircos.Set.Zoom.Plot.Positions.Rd
man/RCircos.Get.Data.Point.Height.Rd
man/RCircos.Data.Point.Rd
RCircos documentation built on May 19, 2017, 4:17 p.m.

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