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circlize (version 0.4.16)

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

34,353

Version

0.4.16

License

MIT + file LICENSE

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Repository

https://github.com/jokergoo/circlize

Homepage

https://jokergoo.github.io/circlize_book/book/

Maintainer

Last Published

February 20th, 2024

Functions in circlize (0.4.16)

chordDiagramFromMatrix

Plot Chord Diagram from an adjacency matrix

adjacencyList2Matrix

Convert adjacency list to an adjacency matrix

arrange_links_evenly

Arrange links evenly on each sector

Easy way to get meta data in the current cell

add_transparency

Add transparency to colors

Plot Chord Diagram

Draw arrow which is paralle to the circle

circos.dendrogram

Add circular dendrograms

adjacencyMatrix2List

Convert adjacency matrix to an adjacency list

Easy to way to get meta data in the current cell

chordDiagramFromDataFrame

Plot Chord Diagram from a data frame

circos.genomicAxis

Add genomic axes

Reset the circular layout parameters

circos.genomicPoints

Add points to a plotting region, specifically for genomic graphics

circos.genomicLink

Add links from two sets of genomic positions

circos.genomicDensity

Calculate and add genomic density track

circlize-package

Circular visualization in R

Draw connecting lines/ribons between two sets of points

circos.genomicLabels

Add labels to specified genomic regions

circos.genomicRect

Draw rectangle-like grid, specifically for genomic graphics

circos.genomicText

Draw text in a cell, specifically for genomic graphics

circos.genomicIdeogram

Add an ideogram track

circos.genomicInitialize

Initialize circular plot with any genomic data

circos.genomicLines

Add lines to a plotting region, specifically for genomic graphics

circos.initialize

Initialize the circular layout

circos.genomicPosTransformLines

Add genomic position transformation lines between tracks

circos.genomicTrack

Create a track for genomic graphics

Convert to polar coordinate system

circos.genomicRainfall

Genomic rainfall plot

circos.genomicTrackPlotRegion

Create a track for genomic graphics

circos.initializeCircularGenome

Initialize a layout for circular genome

Add points to a plotting region

Nested zooming with two circular plots

circos.heatmap.link

Draw a link between two matrix rows in the circular heatmap

Draw text in a cell

Make circular heatmaps

Add a label track

Get information of the circular plot

Draw links between points or/and intervals

Add lines to the plotting region

circos.heatmap.initialize

Initialize circular heatmaps

circos.triangle

circos.initializeWithIdeogram

Initialize the circular layout with an ideogram

Color interpolation

circos.trackPoints

Add points to the plotting regions in a same track

Parameters for the circular layout

circos.segments

Draw segments through pairwise of points

circos.genomicHeatmap

Add heatmaps for selected regions

highlight.sector

Highlight sectors and tracks

Convert unit on x direction in data coordinate

Calculate genomic region density

Add raster images

Draw rectangle-like grid

Convert unit on x direction in data coordinate

circos.trackText

Draw text in cells among the whole track

set.current.cell

Set flag to current cell

Convert unit on x direction in data coordinate

get.all.sector.index

Get index for all sectors

get.current.chromosome

Get current chromosome name

Create plotting regions for a whole track

Draw violin plots

circos.trackLines

Add lines to the plotting regions in a same track

circos.updatePlotRegion

Update the plotting region in an existed cell

circos.trackPlotRegion

Create plotting regions for a whole track

circos.trackHist

Draw histogram in cells among a whole track

get.current.sector.index

Get current sector index

Transform back from colors to values

posTransform.text

Genomic position transformation function specifically for text

Convert unit on y direction in data coordinate

Convert unit on y direction in data coordinate

get_most_inside_radius

Get the inside radius of the most inner track

Convert unit on y direction in data coordinate

rainfallTransform

Calculate inter-distance of genomic regions

Convert fontsize to cex

Convert unit on x direction in data coordinate

Convert unit on y direction in data coordinate

get.all.track.index

Get index for all tracks

get.cell.meta.data

Get the meta data of a cell

Convert unit on x direction in data coordinate

generateRandomBed

Generate random genomic data

Generate random colors

reverse.circlize

Convert to data coordinate system

Mark the value as a degree value

Draw sectors or rings in a circle

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

print.CELL_META

Print CELL_META

Convert unit on y direction in data coordinate

names.CELL_META

Names of all meta data in the current cell

highlight.chromosome

Highlight chromosomes

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

posTransform.default

Genomic position transformation function

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

Create plotting regions for a whole track

get.current.track.index

Get current track index

Convert unit on x direction in data coordinate

Which data that panel.fun is using

Label the sector index and the track index on each cell

Convert unit on y direction in data coordinate

Adjust positions of text

Set gaps between tracks

Calculate gaps to make two Chord diagrams in the same scale