Package: RCircos 1.2.2

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.

Authors:Hongen Zhang

RCircos_1.2.2.tar.gz
RCircos_1.2.2.zip(r-4.7)RCircos_1.2.2.zip(r-4.6)RCircos_1.2.2.zip(r-4.5)
RCircos_1.2.2.tgz(r-4.6-any)RCircos_1.2.2.tgz(r-4.5-any)
RCircos_1.2.2.tar.gz(r-4.7-any)RCircos_1.2.2.tar.gz(r-4.6-any)
RCircos_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
RCircos/json (API)

# Install 'RCircos' in R:

install.packages('RCircos', repos = c('https://hzhanghenry.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hzhanghenry/rcircos/issues

Datasets:

RCircos.Gene.Label.Data - Sample Data for Gene Labels
RCircos.Heatmap.Data - Sample Data for RCircos Heatmap Plot
RCircos.Histogram.Data - Sample Data for RCircos Histogram Plot
RCircos.Line.Data - Sample Data for RCircos Line Plot
RCircos.Link.Data - Sample Data for RCircos Link Plot
RCircos.Mouse.Expr.Data - Sample Data of Mouse Gene Expression
RCircos.Polygon.Data - RCircos Polygon Demo Data
RCircos.Rat.Expr.Data - Sample Data of Rat Gene Expression
RCircos.Ribbon.Data - Sample Data for RCircos Ribbon Plot
RCircos.Scatter.Data - Sample Data for RCircos Scatter Plot
RCircos.Tile.Data - Sample Data for RCircos Tile Plot
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

On CRAN:

7.55 score 6 stars 4 packages 490 scripts 616 downloads 74 mentions 107 exports 0 dependencies

Last updated from:185edece54. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	127
source / vignettes	OK	189
linux-release-x86_64	OK	120
macos-release-arm64	OK	154
macos-oldrel-arm64	OK	136
windows-devel	OK	74
windows-release	OK	76
windows-oldrel	OK	67
wasm-release	OK	94

Dependencies:

Using_RCircos

Rendered fromUsing_RCircos.Rnwusingutils::Sweave

Last update: 2021-12-19
Started: 2021-12-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Circos-like Plot of Genomic Data	RCircos-package RCircos
Adjust Scatter Plot Data to Fit the Data Track	RCircos.Adjust.Scatter.Values
Highlight PLot Area Cross One or More Tracks	RCircos.Area.Highlight
Paint Areas on One Data Track	RCircos.Area.Plot
Plot Chromosome Ideogram	RCircos.Chromosome.Ideogram.Plot RCircos.Draw.Chromosome.Ideogram RCircos.Highligh.Chromosome.Ideogram RCircos.Ideogram.Tick.Plot RCircos.Label.Chromosome.Names
Erase One or More Data Tracks	RCircos.Clear.Track
Erase Zoom-in Plot Area	RCircos.Clear.Zoom.Area
Draw Connectors between Chromosome Ideogram and Gene Names	RCircos.Customized.Connection.Plot
Plot A Customized Shape	RCircos.Customized.Shape.Plot
Convert A Genomic Position to An Index of Circos Plot Position	RCircos.Data.Point
The Default Base Pair Number of A Circos Unit	RCircos.defaultBasePerUnits
Default Character With in Circos Unit	RCircos.defaultCharWidth
The Default Value of GAP in Circos (Chromosome) Unit between two Chromosome Ideogram	RCircos.defaultChromPadding
Default Circos Units for RCircos	RCircos.defaultCircosUnits
Default Character Size of RCircos Plot	RCircos.defaultTextSize
RCircos Environment	RCircos.Env
Draw Connectors between Chromosome Ideogram and Gene Names	RCircos.Gene.Connector.Plot
Sample Data for Gene Labels	RCircos.Gene.Label.Data
Draw Gene Names on a Data Track	RCircos.Gene.Name.Plot
Get Default Coordinates for An Arrow Shape	RCircos.Get.Arrow.Shape
Find the order of Chromosome Names	RCircos.Get.Chromosome.Order
Methods to Retrieve RCircos Core Components Used in Current RCircos Session	RCircos.Get.Plot.Ideogram RCircos.Get.Plot.Parameters RCircos.Get.Plot.Positions
Calculate the Height of Data in A Track	RCircos.Get.Data.Point.Height
Retrieve Parameter Values Stored in RCircos Environment	RCircos.Get.Default.Base.Per.Units RCircos.Get.Default.Char.Width RCircos.Get.Default.Chrom.Padding RCircos.Get.Default.Circos.Units RCircos.Get.Default.Text.Size RCircos.Get.Padding.Constant RCircos.Get.Supported.HeatmapColors RCircos.Get.Supported.Plot.Types
Calculate Plot Positions for Gene Labels	RCircos.Get.Gene.Label.Locations
Calculate Parameters for Gene Name Plot	RCircos.Get.Gene.Name.Plot.Parameters
Generate Color Scales for Heatmap Plot	RCircos.Get.Heatmap.Color.Scale
Calculate X and Y Coordinates for Color Scale	RCircos.Get.Heatmap.Color.Scale.Location
Set Colors for One Track of Heatmap	RCircos.Get.Heatmap.Data.Colors
Set up Colors for Link Lines or Ribbons	RCircos.Get.Link.Colors
Calcualte Plot Positions for A Genomic Interval	RCircos.Get.Paired.Points.Positions
Calculate Boundary of A Data Track	RCircos.Get.Plot.Boundary
Assign Plot Colors for Non-Link Data Plot	RCircos.Get.Plot.Colors
Get the Layer Numbers for Tile Plot	RCircos.Get.Plot.Layers
Calculate the Height of Polygons in A Data Track	RCircos.Get.Polygon.Height
Calculate Plot Positions for Genomic Data	RCircos.Get.Single.Point.Positions
Calculate Start and End Positions for Plot Data	RCircos.Get.Start.End.Locations
Calculate Plot Positions for A Data Track	RCircos.Get.Track.Positions
Retriev Subset of Plot Data for Zoom	RCircos.Get.Zoom.Data
Retrieve Genomic Interval from Genomic Data for Zoom Plot	RCircos.Get.Zoom.Range
Sample Data for RCircos Heatmap Plot	RCircos.Heatmap.Data
Draw Heatmap for One Data Track	RCircos.Heatmap.Plot
Heatmap Colors Supported by Current Version of RCircos	RCircos.heatmapColors
Sample Data for RCircos Histogram Plot	RCircos.Histogram.Data
Plot Histogram for One Data Track	RCircos.Histogram.Plot
Initialize RCircos Plot Parameters	RCircos.Initialize.Plot.Parameters
Sample Data for RCircos Line Plot	RCircos.Line.Data
Draw Lines for One Data Track	RCircos.Line.Plot
Sample Data for RCircos Link Plot	RCircos.Link.Data
Calculate x and y Coordinates for a Bezire Curve	RCircos.Link.Line
Draw Link Lines between Two or More Genomic Positions	RCircos.Link.Plot
List RCircos Plot Parameters	RCircos.List.Plot.Parameters
Sample Data of Mouse Gene Expression	RCircos.Mouse.Expr.Data
Setup RCircos Core Components with Multiple Species Genomes	RCircos.Multiple.Species.Core.Components
Combine Multiple Data Sets form Different Genomes	RCircos.Multiple.Species.Dataset
Padding Distance Constant between Two Chromosomes	RCircos.paddingConst
Draw Lines between Two Genomic Positions on Same Chromosome	RCircos.Parallel.Line.Plot
Plot A Color Scale for Heatmap	RCircos.Plot.Heatmap.Color.Scale
Plot Types Supported by Current RCircos Version	RCircos.plotTypes
Point Plot for One Data Track	RCircos.Point.Plot
RCircos Polygon Demo Data	RCircos.Polygon.Data
Draw Polygons on One Data Track	RCircos.Polygon.Plot
Generate A Pseudo Chromosome Ideogram from List of Lables	RCircos.Pseudo.Ideogram.From.Labels
Generate Pseudo Chromosome Ideogram from Plot Data Table	RCircos.Pseudo.Ideogram.From.Table
Sample Data of Rat Gene Expression	RCircos.Rat.Expr.Data
Reset Methods for Modifying RCircos Core Components	RCircos.Reset.Plot.Ideogram RCircos.Reset.Plot.Parameters RCircos.Reset.Plot.Positions
Sample Data for RCircos Ribbon Plot	RCircos.Ribbon.Data
Draw Ribbon between Two Genomic Regions	RCircos.Ribbon.Plot
Sample Data for RCircos Scatter Plot	RCircos.Scatter.Data
Scater Plot for One Data Track	RCircos.Scatter.Plot
Setup Base Plot Positions	RCircos.Set.Base.Plot.Positions
Initialize Core Components for RCircos Plot	RCircos.Set.Core.Components
Set Chromosome Cytoband Data for Circos Plot	RCircos.Set.Cytoband.Data
Setup Plot Area for RCircos Plot	RCircos.Set.Plot.Area
Set Position for Zoom-in Plot	RCircos.Set.Zoom.Plot.Positions
Sort Genomic or Ideogram Data	RCircos.Sort.Genomic.Data
Sample Data for RCircos Tile Plot	RCircos.Tile.Data
Plot Tiles for One Data Track	RCircos.Tile.Plot
Draw Outline for A Data Track	RCircos.Track.Outline
Validate Chromosome Ideogram Information	RCircos.Validate.Cyto.Info
Validate Genomic Data	RCircos.Validate.Genomic.Data
Validate Genomic Information	RCircos.Validate.Genomic.Info
Validate Plot Parameters	RCircos.Validate.Plot.Parameters
Validate Track Positions	RCircos.Validate.Track.Positions
Draw Vertical Lines on One Data Track	RCircos.Vertical.Line.Plot
A Simple RCircos Plot Workflow	RCircos.Workflow
Draw Outline for Zoom Plot Area	RCircos.Zoom.Area.Outline
Calculate Zoomed Index of Circos Plot Positions for Genomic Intervals	RCircos.Zoom.Paired.Plot.Positions
Calculate Zoomed Index of Circos Plot Positions for Single Point Genomic Data	RCircos.Zoom.Single.Plot.Positions
Zoom in One or Partial Chromosome Ideogram	RCircos.ZoomIn.Chromosome
Zoomed-in Plot of Small Genomic Region	RCircos.Label.Zoom.Region RCircos.Mark.Zoom.Area RCircos.Plot.Zoomed.Area RCircos.Plot.Zoomed.Continue.Lines RCircos.Plot.Zoomed.Gene.Connectors RCircos.Plot.Zoomed.Heatmap RCircos.Plot.Zoomed.Histogram RCircos.Plot.Zoomed.Ideogram.Ticks RCircos.Plot.Zoomed.Parallel.Lines RCircos.Plot.Zoomed.Polygons RCircos.Plot.Zoomed.Scatters RCircos.Plot.Zoomed.Tiles RCircos.Plot.Zoomed.Vertical.Lines
Zoom out Chromosome Ideogram	RCircos.ZoomOut.Chromosome
Cytoband Information for Rat Chromosome Ideogram	UCSC.Baylor.3.4.Rat.cytoBandIdeogram
Cytoband Information for Human Chromosome Ideogram	UCSC.HG19.Human.CytoBandIdeogram
Human Chromosome Ideogram Version 38	UCSC.HG38.Human.CytoBandIdeogram
Cytoband Inforamtion for Mouse Chromosome Ideogram	UCSC.Mouse.GRCm38.CytoBandIdeogram