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circlize (version 0.4.13)

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

29,899

Version

0.4.13

License

MIT + file LICENSE

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Repository

https://github.com/jokergoo/circlize

Homepage

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

Maintainer

Zuguang Gu

Last Published

June 9th, 2021

Functions in circlize (0.4.13)

add_transparency

Add transparency to colors

adjacencyMatrix2List

Convert adjacency matrix to an adjacency list

chordDiagramFromMatrix

Plot Chord Diagram from an adjacency matrix

Easy to way to get meta data in the current cell

Easy way to get meta data in the current cell

arrange_links_evenly

Arrange links evenly on each sector

chordDiagramFromDataFrame

Plot Chord Diagram from a data frame

adjacencyList2Matrix

Convert adjacency list to an adjacency matrix

Calculate gaps to make two Chord diagrams in the same scale

Plot Chord Diagram

circlize-package

Circular visualization in R

Draw arrow which is paralle to the circle

circos.genomicDensity

Calculate and add genomic density track

Convert to polar coordinate system

circos.genomicRainfall

Genomic rainfall plot

circos.genomicPosTransformLines

Add genomic position transformation lines between tracks

Make circular heatmaps

circos.heatmap.initialize

Initialize circular heatmaps

circos.genomicTrack

Create a track for genomic graphics

circos.genomicHeatmap

Add heatmaps for selected regions

circos.genomicTrackPlotRegion

Create a track for genomic graphics

Reset the circular layout parameters

circos.dendrogram

Add circular dendrograms

circos.genomicLink

Add links from two sets of genomic positions

circos.trackHist

Draw histogram in cells among a whole track

Add lines to the plotting region

Add a label track

Draw connecting lines/ribons between two sets of points

Transform back from colors to values

circos.trackLines

Add lines to the plotting regions in a same track

circos.heatmap.link

Draw a link between two matrix rows in the circular heatmap

circos.genomicIdeogram

Add an ideogram track

circos.genomicAxis

Add genomic axes

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.genomicRect

Draw rectangle-like grid, specifically for genomic graphics

circos.genomicText

Draw text in a cell, specifically for genomic graphics

Draw links between points or/and intervals

circos.genomicPoints

Add points to a plotting region, specifically for genomic graphics

circos.trackPlotRegion

Create plotting regions for a whole track

Color interpolation

Draw sectors or rings in a circle

Convert fontsize to cex

Parameters for the circular layout

Draw text in a cell

Create plotting regions for a whole track

Add points to a plotting region

circos.initialize

Initialize the circular layout

circos.trackPoints

Add points to the plotting regions in a same track

circos.initializeWithIdeogram

Initialize the circular layout with an ideogram

circos.segments

Draw segments through pairwise of points

Draw rectangle-like grid

circos.updatePlotRegion

Update the plotting region in an existed cell

Create plotting regions for a whole track

Draw violin plots

Nested zooming with two circular plots

circos.trackText

Draw text in cells among the whole track

get.all.sector.index

Get index for all sectors

get.current.sector.index

Get current sector index

highlight.chromosome

Highlight chromosomes

highlight.sector

Highlight sectors and tracks

Get information of the circular plot

circos.triangle

get.current.track.index

Get current track index

Convert unit on x direction in data coordinate

Convert unit on y direction in data coordinate

generateRandomBed

Generate random genomic data

Calculate genomic region density

Add raster images

Label the sector index and the track index on each cell

Convert unit on y direction in data coordinate

Adjust positions of text

get.all.track.index

Get index for all tracks

Convert unit on x direction in data coordinate

Convert unit on y direction in data coordinate

Mark the value as a degree value

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

Which data that panel.fun is using

Convert unit on y direction in data coordinate

get_most_inside_radius

Get the inside radius of the most inner track

Convert unit on x direction in data coordinate

Generate random colors

Convert unit on x direction in data coordinate

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

set.current.cell

Set flag to current cell

names.CELL_META

Names of all meta data in the current cell

Set gaps between tracks

Convert unit on y direction in data coordinate

Convert unit on x direction in data coordinate

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

Convert unit on y direction in data coordinate

get.cell.meta.data

Get the meta data of a cell

get.current.chromosome

Get current chromosome name

posTransform.default

Genomic position transformation function

reverse.circlize

Convert to data coordinate system

print.CELL_META

Print CELL_META

posTransform.text

Genomic position transformation function specifically for text

rainfallTransform

Calculate inter-distance of genomic regions

Convert unit on x direction in data coordinate