circlize-package: Circular visualization in R

circlize-packageR Documentation

Circular visualization in R

Description

Circular visualization 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 graphic functions:

  • circos.points

  • circos.lines

  • circos.rect

  • circos.polygon

  • circos.segments

  • circos.text

  • circos.axis, circos.xaxis, circos.yaxis

  • circos.barplot

  • circos.boxplot

  • circos.violin

  • circos.link

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

  • circos.trackPoints

  • circos.trackLines

  • circos.trackText

Draw circular heatmaps

  • circos.heatmap

Functions to arrange circular layout:

  • circos.initialize

  • circos.track

  • circos.nested

  • circos.update

  • 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.genomicTrack

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

  • circos.genomicIdeogram

  • circos.genomicHeatmap

  • circos.genomicLabels

Finally, function that draws Chord diagram:

  • chordDiagram

Please refer to the vignettes (https://jokergoo.github.io/circlize_book/book/ ) to find out how to draw basic and advanced circular plots by this package.

Examples

# There is no example
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circlize documentation built on May 11, 2022, 1:06 a.m.