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circlize (version 0.4.10)

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

0.4.10

License

MIT + file LICENSE

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Repository

https://github.com/jokergoo/circlize

Homepage

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

Maintainer

Last Published

June 15th, 2020

Functions in circlize (0.4.10)

Easy to way to get meta data in the current cell

chordDiagramFromMatrix

Plot Chord Diagram from an adjacency matrix

adjacencyList2Matrix

Convert adjacency list to adjacency matrix

Calculate gap to make two Chord diagram with same scale

Plot Chord Diagram

add_transparency

Add transparency to colors

Convert to polar coordinate system

Reset the circular layout parameters

Draw arrow which is paralle to the circle

circos.genomicHeatmap

Add heatmaps for selected regions

circos.genomicLines

Add lines to a plotting region, specifically for genomic graphics

circos.dendrogram

Add circular dendrograms

circos.genomicPoints

Add points to a plotting region, specifically for genomic graphics

circos.genomicPosTransformLines

Add genomic position transformation lines between tracks

circos.genomicLink

Add links from two sets of genomic positions

circos.genomicDensity

Calculate and add genomic density track

circos.genomicText

Draw text in a cell, specifically for genomic graphics

circos.genomicTrack

Create a track for genomic graphics

circos.genomicAxis

Add genomic axes

circos.genomicTrackPlotRegion

Create a track for genomic graphics

Make circular heatmaps

Get information of the circular plot

circos.genomicIdeogram

Add an ideogram track

circos.updatePlotRegion

Update the plotting region in an existed cell

Convert unit on x direction in data coordinate

circos.heatmap.link

Draw a link between two matrix rows in the circular heatmap

Create plotting regions for a whole track

Convert unit on y direction in data coordinate

circos.heatmap.initialize

Initialize circular heatmaps

circos.genomicRainfall

Genomic rainfall plot

get.cell.meta.data

Get the meta data of a cell

circos.genomicInitialize

Initialize circular plot with any genomic data

circos.initialize

Initialize the circular layout

Add raster images

Draw violin plots

Draw text in a cell

circos.genomicLabels

Add labels to specified genomic regions

Add lines to the plotting region

circos.initializeWithIdeogram

Initialize the circular layout with an ideogram

circos.genomicRect

Draw rectangle-like grid, specifically for genomic graphics

Draw rectangle-like grid

circos.trackLines

Add lines to the plotting regions in a same track

Convert unit on y direction in data coordinate

circos.trackHist

Draw histogram in cells among a whole track

reverse.circlize

Convert to data coordinate system

Convert unit on y direction in data coordinate

Convert unit on x direction in data coordinate

Which data that panel.fun is using

get.current.chromosome

Get current chromosome name

circos.segments

Draw segments through pairwise of points

Create plotting regions for a whole track

set.current.cell

Set flag to current cell

rainfallTransform

Calculate inter-distance of genomic regions

Convert unit on x direction in data coordinate

Transform back from colors to values

generateRandomBed

Generate random genomic data

Color interpolation

Convert unit on y direction in data coordinate

Calculate genomic region density

Generate random colors

circos.trackText

Draw text in cells among the whole track

posTransform.default

Genomic position transformation function

names.CELL_META

Names of all meta data in the current cell

get.all.sector.index

Get index for all sectors

Mark the value as a degree value

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

get.all.track.index

Get index for all tracks

Adjust positions of text

circos.triangle

highlight.chromosome

Highlight chromosomes

print.CELL_META

Print CELL_META

posTransform.text

Genomic position transformation function specifically for text

Label the sector index and the track index on each cell

Set gaps between tracks

Add points to a plotting region

Nested zooming with two circular plots

Parameters for the circular layout

Draw links between points or/and intervals

circos.trackPlotRegion

Create plotting regions for a whole track

circos.trackPoints

Add points to the plotting regions in a same track

Draw sectors or rings in a circle

highlight.sector

Highlight sectors and tracks

get.current.track.index

Get current track index

Convert unit on x direction in data coordinate

Convert fontsize to cex

get.current.sector.index

Get current sector index

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

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

Convert unit on x direction in data coordinate

Convert unit on y direction in data coordinate

Convert unit on x direction in data coordinate

Convert unit on y direction in data coordinate

Easy way to get meta data in the current cell

circlize-package

Circular visualization in R

chordDiagramFromDataFrame

Plot Chord Diagram from a data frame