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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>.

Functions (113)

CELL_META

Easy way to get meta data in the current cell

Subset.CELL_META

Easy to way to get meta data in the current cell

add_transparency

Add transparency to colors

adjacencyList2Matrix

Convert adjacency list to an adjacency matrix

adjacencyMatrix2List

Convert adjacency matrix to an adjacency list

arrange_links_evenly

Arrange links evenly on each sector

calc_gap

Calculate gaps to make two Chord diagrams in the same scale

chordDiagram

Plot Chord Diagram

chordDiagramFromDataFrame

Plot Chord Diagram from a data frame

chordDiagramFromMatrix

Plot Chord Diagram from an adjacency matrix

circlize

Convert to polar coordinate system

circlize-package

Circular visualization in R

circos.arrow

Draw arrow which is paralle to the circle

circos.axis

Draw x-axis

circos.barplot

Draw barplots

circos.boxplot

Draw boxplots

circos.clear

Reset the circular layout parameters

circos.connect

Draw connecting lines/ribons between two sets of points

circos.dendrogram

Add circular dendrograms

circos.genomicAxis

Add genomic axes

circos.genomicDensity

Calculate and add genomic density track

circos.genomicHeatmap

Add heatmaps for selected regions

circos.genomicIdeogram

Add an ideogram track

circos.genomicInitialize

Initialize circular plot with any genomic data

circos.genomicLabels

Add labels to specified genomic regions

circos.genomicLines

Add lines to a plotting region, specifically for genomic graphics

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

circos.genomicRect

Draw rectangle-like grid, specifically for genomic graphics

circos.genomicText

Draw text in a cell, specifically for genomic graphics

circos.genomicTrack

Create a track for genomic graphics

circos.genomicTrackPlotRegion

Create a track for genomic graphics

circos.heatmap

Make circular heatmaps

circos.heatmap.initialize

Initialize circular heatmaps

circos.heatmap.link

Draw a link between two matrix rows in the circular heatmap

circos.info

Get information of the circular plot

circos.initialize

Initialize the circular layout

circos.initializeWithIdeogram

Initialize the circular layout with an ideogram

circos.labels

Add a label track

circos.lines

Add lines to the plotting region

circos.link

Draw links between points or/and intervals

circos.nested

Nested zooming with two circular plots

circos.par

Parameters for the circular layout

circos.points

Add points to a plotting region

circos.polygon

Draw polygon

circos.raster

Add raster images

circos.rect

Draw rectangle-like grid

circos.segments

Draw segments through pairwise of points

circos.text

Draw text in a cell

circos.track

Create plotting regions for a whole track

circos.trackHist

Draw histogram in cells among a whole track

circos.trackLines

Add lines to the plotting regions in a same track

circos.trackPlotRegion

Create plotting regions for a whole track

circos.trackPoints

Add points to the plotting regions in a same track

circos.trackText

Draw text in cells among the whole track

circos.triangle

Draw triangles

circos.update

Create plotting regions for a whole track

circos.updatePlotRegion

Update the plotting region in an existed cell

circos.violin

Draw violin plots

circos.xaxis

Draw x-axis

circos.yaxis

Draw y-axis

cm_h

Convert units

cm_x

Convert unit on x direction in data coordinate

cm_y

Convert unit on y direction in data coordinate

col2value

Transform back from colors to values

colorRamp2

Color interpolation

convert_height

Convert units

convert_length

Convert units

convert_x

Convert unit on x direction in data coordinate

convert_y

Convert unit on y direction in data coordinate

cytoband.col

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

degree

Mark the value as a degree value

draw.sector

Draw sectors or rings in a circle

fontsize

Convert fontsize to cex

generateRandomBed

Generate random genomic data

genomicDensity

Calculate genomic region density

get.all.sector.index

Get index for all sectors

get.all.track.index

Get index for all tracks

get.cell.meta.data

Get the meta data of a cell

get.current.chromosome

Get current chromosome name

get.current.sector.index

Get current sector index

get.current.track.index

Get current track index

getI

Which data that panel.fun is using

get_most_inside_radius

Get the inside radius of the most inner track

highlight.chromosome

Highlight chromosomes

highlight.sector

Highlight sectors and tracks

inch_h

Convert units

inch_x

Convert unit on x direction in data coordinate

inch_y

Convert unit on y direction in data coordinate

inches_h

Convert units

inches_x

Convert unit on x direction in data coordinate

inches_y

Convert unit on y direction in data coordinate

mm_h

Convert units

mm_x

Convert unit on x direction in data coordinate

mm_y

Convert unit on y direction in data coordinate

names.CELL_META

Names of all meta data in the current cell

posTransform.default

Genomic position transformation function

posTransform.text

Genomic position transformation function specifically for text

print.CELL_META

Print CELL_META

rainfallTransform

Calculate inter-distance of genomic regions

rand_color

Generate random colors

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

reverse.circlize

Convert to data coordinate system

set.current.cell

Set flag to current cell

set_track_gap

Set gaps between tracks

show.index

Label the sector index and the track index on each cell

smartAlign

Adjust positions of text

uh

Convert units

ux

Convert unit on x direction in data coordinate

uy

Convert unit on y direction in data coordinate

circlize

Circular Visualization

v0.4.12
MIT + file LICENSE
Authors
Zuguang Gu
Initial release
2021-1-8

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