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circlize (version 0.4.17)

Circular Visualization

Description

Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 .

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install.packages('circlize')

Monthly Downloads

47,790

Version

0.4.17

License

MIT + file LICENSE

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Maintainer

Zuguang Gu

Last Published

December 8th, 2025

Functions in circlize (0.4.17)

circos.connect

Draw connecting lines/ribons between two sets of points
circlize-package

Circular visualization in R
circos.barplot

Draw barplots
circos.axis

Draw x-axis
circos.clear

Reset the circular layout parameters
circos.arrow

Draw arrow which is paralle to the circle
circos.dendrogram

Add circular dendrograms
circos.genomicAxis

Add genomic axes
circlize

Convert to polar coordinate system
circos.boxplot

Draw boxplots
circos.genomicLink

Add links from two sets of genomic positions
circos.genomicRainfall

Genomic rainfall plot
circos.genomicPosTransformLines

Add genomic position transformation lines between tracks
circos.genomicDensity

Calculate and add genomic density track
circos.genomicHeatmap

Add heatmaps for selected regions
circos.genomicInitialize

Initialize circular plot with any genomic data
circos.genomicIdeogram

Add an ideogram track
circos.genomicLines

Add lines to a plotting region, specifically for genomic graphics
circos.genomicLabels

Add labels to specified genomic regions
circos.genomicPoints

Add points to a plotting region, specifically for genomic graphics
circos.heatmap.initialize

Initialize circular heatmaps
circos.heatmap

Make circular heatmaps
circos.genomicTrack

Create a track for genomic graphics
circos.genomicTrackPlotRegion

Create a track for genomic graphics
circos.genomicText

Draw text in a cell, specifically for genomic graphics
circos.info

Get information of the circular plot
circos.initialize

Initialize the circular layout
circos.heatmap.link

Draw a link between two matrix rows in the circular heatmap
circos.genomicRect

Draw rectangle-like grid, specifically for genomic graphics
circos.heatmap.get.x

Get the x-position for heatmap rows
circos.points

Add points to a plotting region
circos.polygon

Draw polygon
circos.initializeWithIdeogram

Initialize the circular layout with an ideogram
circos.nested

Nested zooming with two circular plots
circos.raster

Add raster images
circos.par

Parameters for the circular layout
circos.initializeCircularGenome

Initialize a layout for circular genome
circos.lines

Add lines to the plotting region
circos.labels

Add a label track
circos.link

Draw links between points or/and intervals
circos.rect

Draw rectangle-like grid
circos.trackHist

Draw histogram in cells among a whole track
circos.track

Create plotting regions for a whole track
circos.segments

Draw segments through pairwise of points
circos.trackText

Draw text in cells among the whole track
circos.trackPoints

Add points to the plotting regions in a same track
circos.stackedText

Add a stacked text track
circos.trackLines

Add lines to the plotting regions in a same track
circos.text

Draw text in a cell
circos.trackPlotRegion

Create plotting regions for a whole track
cm_x

Convert unit on x direction in data coordinate
cm_h

Convert units
circos.update

Create plotting regions for a whole track
circos.updatePlotRegion

Update the plotting region in an existed cell
circos.yaxis

Draw y-axis
col2value

Transform back from colors to values
circos.triangle

Draw triangles
circos.xaxis

Draw x-axis
cm_y

Convert unit on y direction in data coordinate
circos.violin

Draw violin plots
fontsize

Convert fontsize to cex
colorRamp2

Color interpolation
degree

Mark the value as a degree value
draw.sector

Draw sectors or rings in a circle
convert_y

Convert unit on y direction in data coordinate
cytoband.col

Assign colors to cytogenetic band (hg19) according to the Giemsa stain results
generateRandomBed

Generate random genomic data
get.all.track.index

Get index for all tracks
get.all.sector.index

Get index for all sectors
get.cell.meta.data

Get the meta data of a cell
genomicDensity

Calculate genomic region density
get.current.sector.index

Get current sector index
get.current.chromosome

Get current chromosome name
get.current.track.index

Get current track index
convert_height

Convert units
getI

Which data that panel.fun is using
inches_y

Convert unit on y direction in data coordinate
mm_h

Convert units
convert_x

Convert unit on x direction in data coordinate
mm_x

Convert unit on x direction in data coordinate
convert_length

Convert units
get_most_inside_radius

Get the inside radius of the most inner track
highlight.chromosome

Highlight chromosomes
inches_h

Convert units
inches_x

Convert unit on x direction in data coordinate
inch_y

Convert unit on y direction in data coordinate
posTransform.default

Genomic position transformation function
names.CELL_META

Names of all meta data in the current cell
set.current.cell

Set flag to current cell
reverse.circlize

Convert to data coordinate system
read.chromInfo

Read/parse chromInfo data from a data frame/file/UCSC database
read.cytoband

Read/parse cytoband data from a data frame/file/UCSC database
inch_x

Convert unit on x direction in data coordinate
highlight.sector

Highlight sectors and tracks
inch_h

Convert units
print.CELL_META

Print CELL_META
set_track_gap

Set gaps between tracks
posTransform.text

Genomic position transformation function specifically for text
mm_y

Convert unit on y direction in data coordinate
show.index

Label the sector index and the track index on each cell
smartAlign

Adjust positions of text
uh

Convert units
rainfallTransform

Calculate inter-distance of genomic regions
rand_color

Generate random colors
ux

Convert unit on x direction in data coordinate
uy

Convert unit on y direction in data coordinate
arrange_links_evenly

Arrange links evenly on each sector
calc_gap

Calculate gaps to make two Chord diagrams in the same scale
CELL_META

Easy way to get meta data in the current cell
chordDiagramFromDataFrame

Plot Chord Diagram from a data frame
$.CELL_META

Easy to way to get meta data in the current cell
adjacencyMatrix2List

Convert adjacency matrix to an adjacency list
adjacencyList2Matrix

Convert adjacency list to an adjacency matrix
chordDiagramFromMatrix

Plot Chord Diagram from an adjacency matrix
add_transparency

Add transparency to colors
chordDiagram

Plot Chord Diagram