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-4.5)RCircos_1.2.2.zip(r-4.4)RCircos_1.2.2.zip(r-4.3)
RCircos_1.2.2.tgz(r-4.4-any)RCircos_1.2.2.tgz(r-4.3-any)
RCircos_1.2.2.tar.gz(r-4.5-noble)RCircos_1.2.2.tar.gz(r-4.4-noble)
RCircos_1.2.2.tgz(r-4.4-emscripten)RCircos_1.2.2.tgz(r-4.3-emscripten)
RCircos.pdf |RCircos.html✨
RCircos/json (API)

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

Peer review:

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

Datasets:

On CRAN:

107 exports 6 stars 5.70 score 0 dependencies 3 dependents 74 mentions 296 scripts 781 downloads

Last updated 3 years agofrom:185edece54. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 20 2024
R-4.5-winOKAug 20 2024
R-4.5-linuxOKAug 20 2024
R-4.4-winOKAug 20 2024
R-4.4-macOKAug 20 2024
R-4.3-winOKAug 20 2024
R-4.3-macOKAug 20 2024

Exports:RCircos.Adjust.Scatter.ValuesRCircos.Area.HighlightRCircos.Area.PlotRCircos.Chromosome.Ideogram.PlotRCircos.Clear.TrackRCircos.Clear.Zoom.AreaRCircos.Customized.Connection.PlotRCircos.Customized.Shape.PlotRCircos.Data.PointRCircos.defaultBasePerUnitsRCircos.defaultCharWidthRCircos.defaultChromPaddingRCircos.defaultCircosUnitsRCircos.defaultTextSizeRCircos.Draw.Chromosome.IdeogramRCircos.EnvRCircos.Gene.Connector.PlotRCircos.Gene.Name.PlotRCircos.Get.Arrow.ShapeRCircos.Get.Chromosome.OrderRCircos.Get.Data.Point.HeightRCircos.Get.Default.Base.Per.UnitsRCircos.Get.Default.Char.WidthRCircos.Get.Default.Chrom.PaddingRCircos.Get.Default.Circos.UnitsRCircos.Get.Default.Text.SizeRCircos.Get.Gene.Label.LocationsRCircos.Get.Gene.Name.Plot.ParametersRCircos.Get.Heatmap.Color.ScaleRCircos.Get.Heatmap.Color.Scale.LocationRCircos.Get.Heatmap.Data.ColorsRCircos.Get.Link.ColorsRCircos.Get.Padding.ConstantRCircos.Get.Paired.Points.PositionsRCircos.Get.Plot.BoundaryRCircos.Get.Plot.ColorsRCircos.Get.Plot.IdeogramRCircos.Get.Plot.LayersRCircos.Get.Plot.ParametersRCircos.Get.Plot.PositionsRCircos.Get.Polygon.HeightRCircos.Get.Single.Point.PositionsRCircos.Get.Start.End.LocationsRCircos.Get.Supported.HeatmapColorsRCircos.Get.Supported.Plot.TypesRCircos.Get.Track.PositionsRCircos.Get.Zoom.DataRCircos.Get.Zoom.RangeRCircos.Heatmap.PlotRCircos.heatmapColorsRCircos.Highligh.Chromosome.IdeogramRCircos.Histogram.PlotRCircos.Ideogram.Tick.PlotRCircos.Initialize.Plot.ParametersRCircos.Label.Chromosome.NamesRCircos.Label.Zoom.RegionRCircos.Line.PlotRCircos.Link.LineRCircos.Link.PlotRCircos.List.Plot.ParametersRCircos.Mark.Zoom.AreaRCircos.Multiple.Species.Core.ComponentsRCircos.Multiple.Species.DatasetRCircos.paddingConstRCircos.Parallel.Line.PlotRCircos.Plot.Heatmap.Color.ScaleRCircos.Plot.Zoomed.AreaRCircos.Plot.Zoomed.Continue.LinesRCircos.Plot.Zoomed.Gene.ConnectorsRCircos.Plot.Zoomed.HeatmapRCircos.Plot.Zoomed.HistogramRCircos.Plot.Zoomed.Ideogram.TicksRCircos.Plot.Zoomed.Parallel.LinesRCircos.Plot.Zoomed.PolygonsRCircos.Plot.Zoomed.ScattersRCircos.Plot.Zoomed.TilesRCircos.Plot.Zoomed.Vertical.LinesRCircos.plotTypesRCircos.Point.PlotRCircos.Polygon.PlotRCircos.Pseudo.Ideogram.From.LabelsRCircos.Pseudo.Ideogram.From.TableRCircos.Reset.Plot.IdeogramRCircos.Reset.Plot.ParametersRCircos.Reset.Plot.PositionsRCircos.Ribbon.PlotRCircos.Scatter.PlotRCircos.Set.Base.Plot.PositionsRCircos.Set.Core.ComponentsRCircos.Set.Cytoband.DataRCircos.Set.Plot.AreaRCircos.Set.Zoom.Plot.PositionsRCircos.Sort.Genomic.DataRCircos.Tile.PlotRCircos.Track.OutlineRCircos.Validate.Cyto.InfoRCircos.Validate.Genomic.DataRCircos.Validate.Genomic.InfoRCircos.Validate.Plot.ParametersRCircos.Validate.Track.PositionsRCircos.Vertical.Line.PlotRCircos.WorkflowRCircos.Zoom.Area.OutlineRCircos.Zoom.Paired.Plot.PositionsRCircos.Zoom.Single.Plot.PositionsRCircos.ZoomIn.ChromosomeRCircos.ZoomOut.Chromosome

Dependencies:

Using_RCircos

Rendered fromUsing_RCircos.Rnwusingutils::Sweaveon Aug 20 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Circos-like Plot of Genomic DataRCircos-package RCircos
Adjust Scatter Plot Data to Fit the Data TrackRCircos.Adjust.Scatter.Values
Highlight PLot Area Cross One or More TracksRCircos.Area.Highlight
Paint Areas on One Data TrackRCircos.Area.Plot
Plot Chromosome IdeogramRCircos.Chromosome.Ideogram.Plot RCircos.Draw.Chromosome.Ideogram RCircos.Highligh.Chromosome.Ideogram RCircos.Ideogram.Tick.Plot RCircos.Label.Chromosome.Names
Erase One or More Data TracksRCircos.Clear.Track
Erase Zoom-in Plot AreaRCircos.Clear.Zoom.Area
Draw Connectors between Chromosome Ideogram and Gene NamesRCircos.Customized.Connection.Plot
Plot A Customized ShapeRCircos.Customized.Shape.Plot
Convert A Genomic Position to An Index of Circos Plot PositionRCircos.Data.Point
The Default Base Pair Number of A Circos UnitRCircos.defaultBasePerUnits
Default Character With in Circos UnitRCircos.defaultCharWidth
The Default Value of GAP in Circos (Chromosome) Unit between two Chromosome IdeogramRCircos.defaultChromPadding
Default Circos Units for RCircosRCircos.defaultCircosUnits
Default Character Size of RCircos PlotRCircos.defaultTextSize
RCircos EnvironmentRCircos.Env
Draw Connectors between Chromosome Ideogram and Gene NamesRCircos.Gene.Connector.Plot
Sample Data for Gene LabelsRCircos.Gene.Label.Data
Draw Gene Names on a Data TrackRCircos.Gene.Name.Plot
Get Default Coordinates for An Arrow ShapeRCircos.Get.Arrow.Shape
Find the order of Chromosome NamesRCircos.Get.Chromosome.Order
Methods to Retrieve RCircos Core Components Used in Current RCircos SessionRCircos.Get.Plot.Ideogram RCircos.Get.Plot.Parameters RCircos.Get.Plot.Positions
Calculate the Height of Data in A TrackRCircos.Get.Data.Point.Height
Retrieve Parameter Values Stored in RCircos EnvironmentRCircos.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 LabelsRCircos.Get.Gene.Label.Locations
Calculate Parameters for Gene Name PlotRCircos.Get.Gene.Name.Plot.Parameters
Generate Color Scales for Heatmap PlotRCircos.Get.Heatmap.Color.Scale
Calculate X and Y Coordinates for Color ScaleRCircos.Get.Heatmap.Color.Scale.Location
Set Colors for One Track of HeatmapRCircos.Get.Heatmap.Data.Colors
Set up Colors for Link Lines or RibbonsRCircos.Get.Link.Colors
Calcualte Plot Positions for A Genomic IntervalRCircos.Get.Paired.Points.Positions
Calculate Boundary of A Data TrackRCircos.Get.Plot.Boundary
Assign Plot Colors for Non-Link Data PlotRCircos.Get.Plot.Colors
Get the Layer Numbers for Tile PlotRCircos.Get.Plot.Layers
Calculate the Height of Polygons in A Data TrackRCircos.Get.Polygon.Height
Calculate Plot Positions for Genomic DataRCircos.Get.Single.Point.Positions
Calculate Start and End Positions for Plot DataRCircos.Get.Start.End.Locations
Calculate Plot Positions for A Data TrackRCircos.Get.Track.Positions
Retriev Subset of Plot Data for ZoomRCircos.Get.Zoom.Data
Retrieve Genomic Interval from Genomic Data for Zoom PlotRCircos.Get.Zoom.Range
Sample Data for RCircos Heatmap PlotRCircos.Heatmap.Data
Draw Heatmap for One Data TrackRCircos.Heatmap.Plot
Heatmap Colors Supported by Current Version of RCircosRCircos.heatmapColors
Sample Data for RCircos Histogram PlotRCircos.Histogram.Data
Plot Histogram for One Data TrackRCircos.Histogram.Plot
Initialize RCircos Plot ParametersRCircos.Initialize.Plot.Parameters
Sample Data for RCircos Line PlotRCircos.Line.Data
Draw Lines for One Data TrackRCircos.Line.Plot
Sample Data for RCircos Link PlotRCircos.Link.Data
Calculate x and y Coordinates for a Bezire CurveRCircos.Link.Line
Draw Link Lines between Two or More Genomic PositionsRCircos.Link.Plot
List RCircos Plot ParametersRCircos.List.Plot.Parameters
Sample Data of Mouse Gene ExpressionRCircos.Mouse.Expr.Data
Setup RCircos Core Components with Multiple Species GenomesRCircos.Multiple.Species.Core.Components
Combine Multiple Data Sets form Different GenomesRCircos.Multiple.Species.Dataset
Padding Distance Constant between Two ChromosomesRCircos.paddingConst
Draw Lines between Two Genomic Positions on Same ChromosomeRCircos.Parallel.Line.Plot
Plot A Color Scale for HeatmapRCircos.Plot.Heatmap.Color.Scale
Plot Types Supported by Current RCircos VersionRCircos.plotTypes
Point Plot for One Data TrackRCircos.Point.Plot
RCircos Polygon Demo DataRCircos.Polygon.Data
Draw Polygons on One Data TrackRCircos.Polygon.Plot
Generate A Pseudo Chromosome Ideogram from List of LablesRCircos.Pseudo.Ideogram.From.Labels
Generate Pseudo Chromosome Ideogram from Plot Data TableRCircos.Pseudo.Ideogram.From.Table
Sample Data of Rat Gene ExpressionRCircos.Rat.Expr.Data
Reset Methods for Modifying RCircos Core ComponentsRCircos.Reset.Plot.Ideogram RCircos.Reset.Plot.Parameters RCircos.Reset.Plot.Positions
Sample Data for RCircos Ribbon PlotRCircos.Ribbon.Data
Draw Ribbon between Two Genomic RegionsRCircos.Ribbon.Plot
Sample Data for RCircos Scatter PlotRCircos.Scatter.Data
Scater Plot for One Data TrackRCircos.Scatter.Plot
Setup Base Plot PositionsRCircos.Set.Base.Plot.Positions
Initialize Core Components for RCircos PlotRCircos.Set.Core.Components
Set Chromosome Cytoband Data for Circos PlotRCircos.Set.Cytoband.Data
Setup Plot Area for RCircos PlotRCircos.Set.Plot.Area
Set Position for Zoom-in PlotRCircos.Set.Zoom.Plot.Positions
Sort Genomic or Ideogram DataRCircos.Sort.Genomic.Data
Sample Data for RCircos Tile PlotRCircos.Tile.Data
Plot Tiles for One Data TrackRCircos.Tile.Plot
Draw Outline for A Data TrackRCircos.Track.Outline
Validate Chromosome Ideogram InformationRCircos.Validate.Cyto.Info
Validate Genomic DataRCircos.Validate.Genomic.Data
Validate Genomic InformationRCircos.Validate.Genomic.Info
Validate Plot ParametersRCircos.Validate.Plot.Parameters
Validate Track PositionsRCircos.Validate.Track.Positions
Draw Vertical Lines on One Data TrackRCircos.Vertical.Line.Plot
A Simple RCircos Plot WorkflowRCircos.Workflow
Draw Outline for Zoom Plot AreaRCircos.Zoom.Area.Outline
Calculate Zoomed Index of Circos Plot Positions for Genomic IntervalsRCircos.Zoom.Paired.Plot.Positions
Calculate Zoomed Index of Circos Plot Positions for Single Point Genomic DataRCircos.Zoom.Single.Plot.Positions
Zoom in One or Partial Chromosome IdeogramRCircos.ZoomIn.Chromosome
Zoomed-in Plot of Small Genomic RegionRCircos.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 IdeogramRCircos.ZoomOut.Chromosome
Cytoband Information for Rat Chromosome IdeogramUCSC.Baylor.3.4.Rat.cytoBandIdeogram
Cytoband Information for Human Chromosome IdeogramUCSC.HG19.Human.CytoBandIdeogram
Human Chromosome Ideogram Version 38UCSC.HG38.Human.CytoBandIdeogram
Cytoband Inforamtion for Mouse Chromosome IdeogramUCSC.Mouse.GRCm38.CytoBandIdeogram