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circlize (version 0.4.14)

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

install.packages('circlize')

Monthly Downloads

31,424

Version

0.4.14

License

MIT + file LICENSE

Issues

65

Pull Requests

1

Stars

988

Forks

151

Maintainer

Zuguang Gu

Last Published

February 11th, 2022

Functions in circlize (0.4.14)

adjacencyMatrix2List

Convert adjacency matrix to an adjacency list
CELL_META

Easy way to get meta data in the current cell
calc_gap

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

Add transparency to colors
chordDiagramFromDataFrame

Plot Chord Diagram from a data frame
$.CELL_META

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

Plot Chord Diagram from an adjacency matrix
arrange_links_evenly

Arrange links evenly on each sector
chordDiagram

Plot Chord Diagram
adjacencyList2Matrix

Convert adjacency list to an adjacency matrix
circos.genomicLabels

Add labels to specified genomic regions
circos.barplot

Draw barplots
circos.boxplot

Draw boxplots
circos.initialize

Initialize the circular layout
circos.initializeCircularGenome

Initialize a layout for circular genome
circos.genomicLines

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

Add genomic axes
circos.genomicRect

Draw rectangle-like grid, specifically for genomic graphics
circos.dendrogram

Add circular dendrograms
circos.genomicText

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

Calculate and add genomic density track
circos.connect

Draw connecting lines/ribons between two sets of points
circos.clear

Reset the circular layout parameters
circos.arrow

Draw arrow which is paralle to the circle
circos.genomicInitialize

Initialize circular plot with any genomic data
circos.genomicIdeogram

Add an ideogram track
circos.genomicHeatmap

Add heatmaps for selected regions
circos.raster

Add raster images
circos.points

Add points to a plotting region
circos.nested

Nested zooming with two circular plots
circos.heatmap

Make circular heatmaps
circos.heatmap.initialize

Initialize circular heatmaps
circos.trackLines

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

Draw polygon
circos.rect

Draw rectangle-like grid
circos.text

Draw text in a cell
circos.segments

Draw segments through pairwise of points
circlize-package

Circular visualization in R
circos.axis

Draw x-axis
circlize

Convert to polar coordinate system
circos.genomicLink

Add links from two sets of genomic positions
circos.genomicPoints

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

Add genomic position transformation lines between tracks
circos.genomicRainfall

Genomic rainfall plot
convert_height

Convert units
draw.sector

Draw sectors or rings in a circle
colorRamp2

Color interpolation
degree

Mark the value as a degree value
circos.genomicTrack

Create a track for genomic graphics
circos.par

Parameters for the circular layout
circos.genomicTrackPlotRegion

Create a track for genomic graphics
highlight.sector

Highlight sectors and tracks
circos.initializeWithIdeogram

Initialize the circular layout with an ideogram
circos.labels

Add a label track
cm_y

Convert unit on y direction in data coordinate
circos.trackPlotRegion

Create plotting regions for a whole track
col2value

Transform back from colors to values
convert_y

Convert unit on y direction in data coordinate
circos.lines

Add lines to the plotting region
circos.heatmap.link

Draw a link between two matrix rows in the circular heatmap
cm_h

Convert units
cm_x

Convert unit on x direction in data coordinate
inch_h

Convert units
get.all.sector.index

Get index for all sectors
getI

Which data that panel.fun is using
genomicDensity

Calculate genomic region density
get.current.track.index

Get current track index
inches_y

Convert unit on y direction in data coordinate
get_most_inside_radius

Get the inside radius of the most inner track
cytoband.col

Assign colors to cytogenetic band (hg19) according to the Giemsa stain results
highlight.chromosome

Highlight chromosomes
circos.trackHist

Draw histogram in cells among a whole track
circos.track

Create plotting regions for a whole track
circos.link

Draw links between points or/and intervals
names.CELL_META

Names of all meta data in the current cell
circos.info

Get information of the circular plot
mm_h

Convert units
generateRandomBed

Generate random genomic data
get.current.sector.index

Get current sector index
circos.update

Create plotting regions for a whole track
get.current.chromosome

Get current chromosome name
circos.triangle

Draw triangles
fontsize

Convert fontsize to cex
circos.trackText

Draw text in cells among the whole track
circos.trackPoints

Add points to the plotting regions in a same track
inch_x

Convert unit on x direction in data coordinate
mm_x

Convert unit on x direction in data coordinate
mm_y

Convert unit on y direction in data coordinate
circos.updatePlotRegion

Update the plotting region in an existed cell
posTransform.default

Genomic position transformation function
inch_y

Convert unit on y direction in data coordinate
read.chromInfo

Read/parse chromInfo data from a data frame/file/UCSC database
rainfallTransform

Calculate inter-distance of genomic regions
rand_color

Generate random colors
circos.violin

Draw violin plots
print.CELL_META

Print CELL_META
posTransform.text

Genomic position transformation function specifically for text
circos.xaxis

Draw x-axis
read.cytoband

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

Adjust positions of text
ux

Convert unit on x direction in data coordinate
convert_length

Convert units
circos.yaxis

Draw y-axis
convert_x

Convert unit on x direction in data coordinate
get.all.track.index

Get index for all tracks
inches_h

Convert units
get.cell.meta.data

Get the meta data of a cell
uh

Convert units
uy

Convert unit on y direction in data coordinate
set.current.cell

Set flag to current cell
reverse.circlize

Convert to data coordinate system
inches_x

Convert unit on x direction in data coordinate
set_track_gap

Set gaps between tracks
show.index

Label the sector index and the track index on each cell