Circular layout in R

Description

Circular layout in R

Details

This package aims to implement circular layout in R.

Since most of the figures are composed of points, lines and polygons, we just need to implement low-level functions for drawing points, lines and polygons.

Current there are following low-level graphical functions:

• circos.points

• circos.lines

• circos.rect

• circos.polygon

• circos.text

• circos.axis

• circos.link, This maybe the unique feature for circular layout to represent relationships between elements.

For drawing points, lines and text through the whole track (among several sectors), the following functions are available:

• circos.trackPoints

• circos.trackLines

• circos.trackText

Functions to arrange circular layout:

• circos.trackPlotRegion

• circos.updatePlotRegion

• circos.par

• circos.info

• circos.clear

Theoretically, you are able to draw most kinds of circular plots by the above functions.

For specific use in genomics, we also implement functions which add graphics in genome scale.

Functions to initialize circos plot with genomic coordinates:

• circos.initializeWithIdeogram

• circos.genomicInitialize

Functions to arrange genomic circular layout:

• circos.genomicTrackPlotRegion

Functions to add basic graphics in genomic scale:

• circos.genomicPoints

• circos.genomicLines

• circos.genomicText

• circos.genomicRect

• circos.genomicLink

Functions with specific purpose:

• circos.genomicDensity

• circos.genomicRainfall

Finally, function that draws chord diagram:

• chordDiagram

• chordDiagramFromMatrix

• chordDiagramFromDataFrame

Please refer to the vignettes to find out how to draw basic and advanced circular plots by this package.

Examples

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Results