Package: circlize 0.4.16

Zuguang Gu

circlize: Circular Visualization

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 <doi:10.1093/bioinformatics/btu393>.

Authors:Zuguang Gu [aut, cre]

circlize_0.4.16.tar.gz
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circlize_0.4.16.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
circlize/json (API)

# Install 'circlize' in R:

install.packages('circlize', repos = c('https://jokergoo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jokergoo/circlize/issues

On CRAN:

16.28 score 1.0k stars 251 packages 18k scripts 68k downloads 260 mentions 115 exports 3 dependencies

Last updated from:9b2157843e. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	164
source / vignettes	OK	209
linux-release-x86_64	NOTE	152
macos-release-arm64	NOTE	104
macos-oldrel-arm64	NOTE	95
windows-devel	NOTE	124
windows-release	NOTE	158
windows-oldrel	NOTE	113
wasm-release	OK	101

Exports:$.CELL_META add_transparency adjacencyList2Matrix adjacencyMatrix2List arrange_links_evenly calc_gap CELL_META chordDiagram chordDiagramFromDataFrame chordDiagramFromMatrix circlize circos.arrow circos.axis circos.barplot circos.boxplot circos.clear circos.connect circos.dendrogram circos.genomicAxis circos.genomicDensity circos.genomicHeatmap circos.genomicIdeogram circos.genomicInitialize circos.genomicLabels circos.genomicLines circos.genomicLink circos.genomicPoints circos.genomicPosTransformLines circos.genomicRainfall circos.genomicRect circos.genomicText circos.genomicTrack circos.genomicTrackPlotRegion circos.heatmap circos.heatmap.get.x circos.heatmap.initialize circos.heatmap.link circos.info circos.initialize circos.initializeCircularGenome circos.initializeWithIdeogram circos.labels circos.lines circos.link circos.nested circos.par circos.points circos.polygon circos.raster circos.rect circos.segments circos.stackedText circos.text circos.track circos.trackHist circos.trackLines circos.trackPlotRegion circos.trackPoints circos.trackText circos.triangle circos.update circos.updatePlotRegion circos.violin circos.xaxis circos.yaxis cm_h cm_x cm_y col2value colorRamp2 convert_height convert_length convert_x convert_y cytoband.col degree draw.sector fontsize generateRandomBed genomicDensity get_most_inside_radius get.all.sector.index get.all.track.index get.cell.meta.data get.current.chromosome get.current.sector.index get.current.track.index getI highlight.chromosome highlight.sector inch_h inch_x inch_y inches_h inches_x inches_y mm_h mm_x mm_y names.CELL_META posTransform.default posTransform.text print.CELL_META rainfallTransform rand_color read.chromInfo read.cytoband reverse.circlize set_track_gap set.current.cell show.index smartAlign uh ux uy

Dependencies:colorspace GlobalOptions shape

circlize vignette

Rendered fromcirclize.Rmdusingknitr

Last update: 2020-06-14
Started: 2017-11-06

Help page	Topics
Circular visualization in R	circlize-package
Easy to way to get meta data in the current cell	$.CELL_META Subset.CELL_META
Add transparency to colors	add_transparency
Convert adjacency list to an adjacency matrix	adjacencyList2Matrix
Convert adjacency matrix to an adjacency list	adjacencyMatrix2List
Arrange links evenly on each sector	arrange_links_evenly
Calculate gaps to make two Chord diagrams in the same scale	calc_gap
Easy way to get meta data in the current cell	CELL_META
Plot Chord Diagram	chordDiagram
Plot Chord Diagram from a data frame	chordDiagramFromDataFrame
Plot Chord Diagram from an adjacency matrix	chordDiagramFromMatrix
Convert to polar coordinate system	circlize
Draw arrow which is paralle to the circle	circos.arrow
Draw x-axis	circos.axis
Draw barplots	circos.barplot
Draw boxplots	circos.boxplot
Reset the circular layout parameters	circos.clear
Draw connecting lines/ribons between two sets of points	circos.connect
Add circular dendrograms	circos.dendrogram
Add genomic axes	circos.genomicAxis
Calculate and add genomic density track	circos.genomicDensity
Add heatmaps for selected regions	circos.genomicHeatmap
Add an ideogram track	circos.genomicIdeogram
Initialize circular plot with any genomic data	circos.genomicInitialize
Add labels to specified genomic regions	circos.genomicLabels
Add lines to a plotting region, specifically for genomic graphics	circos.genomicLines
Add links from two sets of genomic positions	circos.genomicLink
Add points to a plotting region, specifically for genomic graphics	circos.genomicPoints
Add genomic position transformation lines between tracks	circos.genomicPosTransformLines
Genomic rainfall plot	circos.genomicRainfall
Draw rectangle-like grid, specifically for genomic graphics	circos.genomicRect
Draw text in a cell, specifically for genomic graphics	circos.genomicText
Create a track for genomic graphics	circos.genomicTrack
Create a track for genomic graphics	circos.genomicTrackPlotRegion
Make circular heatmaps	circos.heatmap
Get the x-position for heatmap rows	circos.heatmap.get.x
Initialize circular heatmaps	circos.heatmap.initialize
Draw a link between two matrix rows in the circular heatmap	circos.heatmap.link
Get information of the circular plot	circos.info
Initialize the circular layout	circos.initialize
Initialize a layout for circular genome	circos.initializeCircularGenome
Initialize the circular layout with an ideogram	circos.initializeWithIdeogram
Add a label track	circos.labels
Add lines to the plotting region	circos.lines
Draw links between points or/and intervals	circos.link
Nested zooming with two circular plots	circos.nested
Parameters for the circular layout	circos.par
Add points to a plotting region	circos.points
Draw polygon	circos.polygon
Add raster images	circos.raster
Draw rectangle-like grid	circos.rect
Draw segments through pairwise of points	circos.segments
Add a stacked text track	circos.stackedText
Draw text in a cell	circos.text
Create plotting regions for a whole track	circos.track
Draw histogram in cells among a whole track	circos.trackHist
Add lines to the plotting regions in a same track	circos.trackLines
Create plotting regions for a whole track	circos.trackPlotRegion
Add points to the plotting regions in a same track	circos.trackPoints
Draw text in cells among the whole track	circos.trackText
Draw triangles	circos.triangle
Create plotting regions for a whole track	circos.update
Update the plotting region in an existed cell	circos.updatePlotRegion
Draw violin plots	circos.violin
Draw x-axis	circos.xaxis
Draw y-axis	circos.yaxis
Convert units	cm_h
Convert unit on x direction in data coordinate	cm_x
Convert unit on y direction in data coordinate	cm_y
Transform back from colors to values	col2value
Color interpolation	colorRamp2
Convert units	convert_height
Convert units	convert_length
Convert unit on x direction in data coordinate	convert_x
Convert unit on y direction in data coordinate	convert_y
Assign colors to cytogenetic band (hg19) according to the Giemsa stain results	cytoband.col
Mark the value as a degree value	degree
Draw sectors or rings in a circle	draw.sector
Convert fontsize to cex	fontsize
Generate random genomic data	generateRandomBed
Calculate genomic region density	genomicDensity
Get the inside radius of the most inner track	get_most_inside_radius
Get index for all sectors	get.all.sector.index
Get index for all tracks	get.all.track.index
Get the meta data of a cell	get.cell.meta.data
Get current chromosome name	get.current.chromosome
Get current sector index	get.current.sector.index
Get current track index	get.current.track.index
Which data that 'panel.fun' is using	getI
Highlight chromosomes	highlight.chromosome
Highlight sectors and tracks	highlight.sector
Convert units	inch_h
Convert unit on x direction in data coordinate	inch_x
Convert unit on y direction in data coordinate	inch_y
Convert units	inches_h
Convert unit on x direction in data coordinate	inches_x
Convert unit on y direction in data coordinate	inches_y
Convert units	mm_h
Convert unit on x direction in data coordinate	mm_x
Convert unit on y direction in data coordinate	mm_y
Names of all meta data in the current cell	names.CELL_META
Genomic position transformation function	posTransform.default
Genomic position transformation function specifically for text	posTransform.text
Print CELL_META	print.CELL_META
Calculate inter-distance of genomic regions	rainfallTransform
Generate random colors	rand_color
Read/parse chromInfo data from a data frame/file/UCSC database	read.chromInfo
Read/parse cytoband data from a data frame/file/UCSC database	read.cytoband
Convert to data coordinate system	reverse.circlize
Set gaps between tracks	set_track_gap
Set flag to current cell	set.current.cell
Label the sector index and the track index on each cell	show.index
Adjust positions of text	smartAlign
Convert units	uh
Convert unit on x direction in data coordinate	ux
Convert unit on y direction in data coordinate	uy

Package: circlize 0.4.16

circlize: Circular Visualization

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