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]

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circlize.pdf |circlize.html✨
circlize/json (API)
NEWS

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

Peer review:

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

On CRAN:

115 exports 958 stars 10.71 score 3 dependencies 192 dependents 260 mentions 8.4k scripts 28.6k downloads

Last updated 10 months agofrom:9b2157843e. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 06 2024
R-4.5-winNOTESep 06 2024
R-4.5-linuxNOTESep 06 2024
R-4.4-winNOTESep 06 2024
R-4.4-macNOTESep 06 2024
R-4.3-winOKSep 06 2024
R-4.3-macOKSep 06 2024

Exports:$.CELL_METAadd_transparencyadjacencyList2MatrixadjacencyMatrix2Listarrange_links_evenlycalc_gapCELL_METAchordDiagramchordDiagramFromDataFramechordDiagramFromMatrixcirclizecircos.arrowcircos.axiscircos.barplotcircos.boxplotcircos.clearcircos.connectcircos.dendrogramcircos.genomicAxiscircos.genomicDensitycircos.genomicHeatmapcircos.genomicIdeogramcircos.genomicInitializecircos.genomicLabelscircos.genomicLinescircos.genomicLinkcircos.genomicPointscircos.genomicPosTransformLinescircos.genomicRainfallcircos.genomicRectcircos.genomicTextcircos.genomicTrackcircos.genomicTrackPlotRegioncircos.heatmapcircos.heatmap.get.xcircos.heatmap.initializecircos.heatmap.linkcircos.infocircos.initializecircos.initializeCircularGenomecircos.initializeWithIdeogramcircos.labelscircos.linescircos.linkcircos.nestedcircos.parcircos.pointscircos.polygoncircos.rastercircos.rectcircos.segmentscircos.stackedTextcircos.textcircos.trackcircos.trackHistcircos.trackLinescircos.trackPlotRegioncircos.trackPointscircos.trackTextcircos.trianglecircos.updatecircos.updatePlotRegioncircos.violincircos.xaxiscircos.yaxiscm_hcm_xcm_ycol2valuecolorRamp2convert_heightconvert_lengthconvert_xconvert_ycytoband.coldegreedraw.sectorfontsizegenerateRandomBedgenomicDensityget_most_inside_radiusget.all.sector.indexget.all.track.indexget.cell.meta.dataget.current.chromosomeget.current.sector.indexget.current.track.indexgetIhighlight.chromosomehighlight.sectorinch_hinch_xinch_yinches_hinches_xinches_ymm_hmm_xmm_ynames.CELL_METAposTransform.defaultposTransform.textprint.CELL_METArainfallTransformrand_colorread.chromInforead.cytobandreverse.circlizeset_track_gapset.current.cellshow.indexsmartAlignuhuxuy

Dependencies:colorspaceGlobalOptionsshape

circlize vignette

Rendered fromcirclize.Rmdusingknitron Sep 06 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Circular visualization in Rcirclize-package
Easy to way to get meta data in the current cell$.CELL_META Subset.CELL_META
Add transparency to colorsadd_transparency
Convert adjacency list to an adjacency matrixadjacencyList2Matrix
Convert adjacency matrix to an adjacency listadjacencyMatrix2List
Arrange links evenly on each sectorarrange_links_evenly
Calculate gaps to make two Chord diagrams in the same scalecalc_gap
Easy way to get meta data in the current cellCELL_META
Plot Chord DiagramchordDiagram
Plot Chord Diagram from a data framechordDiagramFromDataFrame
Plot Chord Diagram from an adjacency matrixchordDiagramFromMatrix
Convert to polar coordinate systemcirclize
Draw arrow which is paralle to the circlecircos.arrow
Draw x-axiscircos.axis
Draw barplotscircos.barplot
Draw boxplotscircos.boxplot
Reset the circular layout parameterscircos.clear
Draw connecting lines/ribons between two sets of pointscircos.connect
Add circular dendrogramscircos.dendrogram
Add genomic axescircos.genomicAxis
Calculate and add genomic density trackcircos.genomicDensity
Add heatmaps for selected regionscircos.genomicHeatmap
Add an ideogram trackcircos.genomicIdeogram
Initialize circular plot with any genomic datacircos.genomicInitialize
Add labels to specified genomic regionscircos.genomicLabels
Add lines to a plotting region, specifically for genomic graphicscircos.genomicLines
Add links from two sets of genomic positionscircos.genomicLink
Add points to a plotting region, specifically for genomic graphicscircos.genomicPoints
Add genomic position transformation lines between trackscircos.genomicPosTransformLines
Genomic rainfall plotcircos.genomicRainfall
Draw rectangle-like grid, specifically for genomic graphicscircos.genomicRect
Draw text in a cell, specifically for genomic graphicscircos.genomicText
Create a track for genomic graphicscircos.genomicTrack
Create a track for genomic graphicscircos.genomicTrackPlotRegion
Make circular heatmapscircos.heatmap
Get the x-position for heatmap rowscircos.heatmap.get.x
Initialize circular heatmapscircos.heatmap.initialize
Draw a link between two matrix rows in the circular heatmapcircos.heatmap.link
Get information of the circular plotcircos.info
Initialize the circular layoutcircos.initialize
Initialize a layout for circular genomecircos.initializeCircularGenome
Initialize the circular layout with an ideogramcircos.initializeWithIdeogram
Add a label trackcircos.labels
Add lines to the plotting regioncircos.lines
Draw links between points or/and intervalscircos.link
Nested zooming with two circular plotscircos.nested
Parameters for the circular layoutcircos.par
Add points to a plotting regioncircos.points
Draw polygoncircos.polygon
Add raster imagescircos.raster
Draw rectangle-like gridcircos.rect
Draw segments through pairwise of pointscircos.segments
Add a stacked text trackcircos.stackedText
Draw text in a cellcircos.text
Create plotting regions for a whole trackcircos.track
Draw histogram in cells among a whole trackcircos.trackHist
Add lines to the plotting regions in a same trackcircos.trackLines
Create plotting regions for a whole trackcircos.trackPlotRegion
Add points to the plotting regions in a same trackcircos.trackPoints
Draw text in cells among the whole trackcircos.trackText
Draw trianglescircos.triangle
Create plotting regions for a whole trackcircos.update
Update the plotting region in an existed cellcircos.updatePlotRegion
Draw violin plotscircos.violin
Draw x-axiscircos.xaxis
Draw y-axiscircos.yaxis
Convert unitscm_h
Convert unit on x direction in data coordinatecm_x
Convert unit on y direction in data coordinatecm_y
Transform back from colors to valuescol2value
Color interpolationcolorRamp2
Convert unitsconvert_height
Convert unitsconvert_length
Convert unit on x direction in data coordinateconvert_x
Convert unit on y direction in data coordinateconvert_y
Assign colors to cytogenetic band (hg19) according to the Giemsa stain resultscytoband.col
Mark the value as a degree valuedegree
Draw sectors or rings in a circledraw.sector
Convert fontsize to cexfontsize
Generate random genomic datagenerateRandomBed
Calculate genomic region densitygenomicDensity
Get the inside radius of the most inner trackget_most_inside_radius
Get index for all sectorsget.all.sector.index
Get index for all tracksget.all.track.index
Get the meta data of a cellget.cell.meta.data
Get current chromosome nameget.current.chromosome
Get current sector indexget.current.sector.index
Get current track indexget.current.track.index
Which data that 'panel.fun' is usinggetI
Highlight chromosomeshighlight.chromosome
Highlight sectors and trackshighlight.sector
Convert unitsinch_h
Convert unit on x direction in data coordinateinch_x
Convert unit on y direction in data coordinateinch_y
Convert unitsinches_h
Convert unit on x direction in data coordinateinches_x
Convert unit on y direction in data coordinateinches_y
Convert unitsmm_h
Convert unit on x direction in data coordinatemm_x
Convert unit on y direction in data coordinatemm_y
Names of all meta data in the current cellnames.CELL_META
Genomic position transformation functionposTransform.default
Genomic position transformation function specifically for textposTransform.text
Print CELL_METAprint.CELL_META
Calculate inter-distance of genomic regionsrainfallTransform
Generate random colorsrand_color
Read/parse chromInfo data from a data frame/file/UCSC databaseread.chromInfo
Read/parse cytoband data from a data frame/file/UCSC databaseread.cytoband
Convert to data coordinate systemreverse.circlize
Set gaps between tracksset_track_gap
Set flag to current cellset.current.cell
Label the sector index and the track index on each cellshow.index
Adjust positions of textsmartAlign
Convert unitsuh
Convert unit on x direction in data coordinateux
Convert unit on y direction in data coordinateuy