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RCircos (version 1.2.1)

Circos 2D Track Plot

Description

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.

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Version

Install

install.packages('RCircos')

Monthly Downloads

827

Version

1.2.1

License

GPL (>= 2)

Maintainer

Hongen Zhang

Last Published

March 12th, 2019

Functions in RCircos (1.2.1)

RCircos.Chromosome.Ideogram.Plot

Plot Chromosome Ideogram
RCircos.Get.Plot.Boundary

Calculate Boundary of A Data Track
RCircos.Get.Plot.Colors

Assign Plot Colors for Non-Link Data Plot
RCircos.Get.Track.Positions

Calculate Plot Positions for A Data Track
RCircos.Get.Zoom.Data

Retriev Subset of Plot Data for Zoom
RCircos.Area.Plot

Paint Areas on One Data Track
RCircos.Area.Highlight

Highlight PLot Area Cross One or More Tracks
RCircos.Get.Core.Components

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.Arrow.Shape

Get Default Coordinates for An Arrow Shape
RCircos-package

Circos-like Plot of Genomic Data
RCircos.Line.Data

Sample Data for RCircos Line Plot
RCircos.Line.Plot

Draw Lines for One Data Track
RCircos.Get.Chromosome.Order

Find the order of Chromosome Names
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.Link.Colors

Set up Colors for Link Lines or Ribbons
RCircos.Adjust.Scatter.Values

Adjust Scatter Plot Data to Fit the Data Track
RCircos.Env

RCircos Environment
RCircos.Get.Zoom.Range

Retrieve Genomic Interval from Genomic Data for Zoom Plot
RCircos.Gene.Connector.Plot

Draw Connectors between Chromosome Ideogram and Gene Names
RCircos.Heatmap.Data

Sample Data for RCircos Heatmap Plot
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.Set.Cytoband.Data

Set Chromosome Cytoband Data for Circos Plot
RCircos.Clear.Zoom.Area

Erase Zoom-in Plot Area
RCircos.Histogram.Plot

Plot Histogram for One Data Track
RCircos.Customized.Shape.Plot

Plot A Customized Shape
RCircos.Set.Plot.Area

Setup Plot Area for RCircos Plot
RCircos.Initialize.Plot.Parameters

Initialize RCircos Plot Parameters
RCircos.Mouse.Expr.Data

Sample Data of Mouse Gene Expression
RCircos.Customized.Connection.Plot

Draw Connectors between Chromosome Ideogram and Gene Names
RCircos.Validate.Plot.Parameters

Validate Plot Parameters
RCircos.Data.Point

Convert A Genomic Position to An Index of Circos Plot Position
RCircos.Get.Paired.Points.Positions

Calcualte Plot Positions for A Genomic Interval
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.Polygon.Plot

Draw Polygons on One Data Track
RCircos.Parallel.Line.Plot

Draw Lines between Two Genomic Positions on Same Chromosome
RCircos.Tile.Plot

Plot Tiles for One Data Track
RCircos.Tile.Data

Sample Data for RCircos Tile Plot
RCircos.Polygon.Data

RCircos Polygon Demo Data
RCircos.Set.Zoom.Plot.Positions

Set Position for Zoom-in Plot
RCircos.defaultChromPadding

The Default Value of GAP in Circos (Chromosome) Unit between two Chromosome Ideogram
RCircos.Validate.Track.Positions

Validate Track Positions
RCircos.Sort.Genomic.Data

Sort Genomic or Ideogram Data
RCircos.Get.Plot.Layers

Get the Layer Numbers for Tile Plot
RCircos.Zoom.Paired.Plot.Positions

Calculate Zoomed Index of Circos Plot Positions for Genomic Intervals
RCircos.Zoom.Area.Outline

Draw Outline for Zoom Plot Area
RCircos.defaultCharWidth

Default Character With in Circos Unit
RCircos.defaultBasePerUnits

The Default Base Pair Number of A Circos Unit
RCircos.Gene.Label.Data

Sample Data for Gene Labels
RCircos.Gene.Name.Plot

Draw Gene Names on a Data Track
RCircos.Get.Polygon.Height

Calculate the Height of Polygons in A Data Track
RCircos.ZoomIn.Plot

Zoomed-in Plot of Small Genomic Region
RCircos.Rat.Expr.Data

Sample Data of Rat Gene Expression
UCSC.Baylor.3.4.Rat.cytoBandIdeogram

Cytoband Information for Rat Chromosome Ideogram
RCircos.ZoomOut.Chromosome

Zoom out Chromosome Ideogram
UCSC.HG19.Human.CytoBandIdeogram

Cytoband Information for Human Chromosome Ideogram
RCircos.Set.Base.Plot.Positions

Setup Base Plot Positions
RCircos.Reset.Core.Components

Reset Methods for Modifying RCircos Core Components
RCircos.Set.Core.Components

Initialize Core Components for RCircos Plot
RCircos.defaultCircosUnits

Default Circos Units for RCircos
RCircos.Get.Single.Point.Positions

Calculate Plot Positions for Genomic Data
RCircos.Validate.Genomic.Data

Validate Genomic Data
RCircos.Get.Heatmap.Color.Scale

Generate Color Scales for Heatmap Plot
RCircos.Get.Start.End.Locations

Calculate Start and End Positions for Plot Data
RCircos.Validate.Genomic.Info

Validate Genomic Information
RCircos.Plot.Heatmap.Color.Scale

Plot A Color Scale for Heatmap
RCircos.List.Plot.Parameters

List RCircos Plot Parameters
RCircos.Link.Plot

Draw Link Lines between Two or More Genomic Positions
RCircos.Get.Heatmap.Data.Colors

Set Colors for One Track of Heatmap
RCircos.Heatmap.Plot

Draw Heatmap for One Data Track
RCircos.Point.Plot

Point Plot for One Data Track
RCircos.Vertical.Line.Plot

Draw Vertical Lines on One Data Track
RCircos.Histogram.Data

Sample Data for RCircos Histogram Plot
RCircos.Workflow

A Simple RCircos Plot Workflow
RCircos.Link.Data

Sample Data for RCircos Link Plot
RCircos.defaultTextSize

Default Character Size of RCircos Plot
RCircos.Link.Line

Calculate x and y Coordinates for a Bezire Curve
RCircos.heatmapColors

Heatmap Colors Supported by Current Version of RCircos
RCircos.Ribbon.Data

Sample Data for RCircos Ribbon Plot
UCSC.HG38.Human.CytoBandIdeogram

Human Chromosome Ideogram Version 38
RCircos.Ribbon.Plot

Draw Ribbon between Two Genomic Regions
UCSC.Mouse.GRCm38.CytoBandIdeogram

Cytoband Inforamtion for Mouse Chromosome Ideogram
RCircos.Scatter.Data

Sample Data for RCircos Scatter Plot
RCircos.Scatter.Plot

Scater Plot for One Data Track
RCircos.Track.Outline

Draw Outline for A Data Track
RCircos.Validate.Cyto.Info

Validate Chromosome Ideogram Information
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.paddingConst

Padding Distance Constant between Two Chromosomes
RCircos.plotTypes

Plot Types Supported by Current RCircos Version
RCircos.Get.Default.Parameters

Retrieve Parameter Values Stored in RCircos Environment
RCircos.Get.Gene.Label.Locations

Calculate Plot Positions for Gene Labels
RCircos.Clear.Track

Erase One or More Data Tracks