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circlize (version 0.4.11)

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

33,668

Version

0.4.11

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

October 31st, 2020

Functions in circlize (0.4.11)

adjacencyList2Matrix

Convert adjacency list to an adjacency matrix

Calculate gaps to make two Chord diagrams in the same scale

add_transparency

Add transparency to colors

Easy way to get meta data in the current cell

circlize-package

Circular visualization in R

Plot Chord Diagram

chordDiagramFromMatrix

Plot Chord Diagram from an adjacency matrix

chordDiagramFromDataFrame

Plot Chord Diagram from a data frame

adjacencyMatrix2List

Convert adjacency matrix to an adjacency list

Easy to way to get meta data in the current cell

circos.genomicIdeogram

Add an ideogram track

circos.genomicInitialize

Initialize circular plot with any genomic data

circos.genomicHeatmap

Add heatmaps for selected regions

circos.genomicText

Draw text in a cell, specifically for genomic graphics

Draw links between points or/and intervals

circos.genomicDensity

Calculate and add genomic density track

circos.genomicRect

Draw rectangle-like grid, specifically for genomic graphics

Add lines to the plotting region

Create plotting regions for a whole track

circos.trackHist

Draw histogram in cells among a whole track

Reset the circular layout parameters

circos.trackLines

Add lines to the plotting regions in a same track

circos.initialize

Initialize the circular layout

circos.initializeWithIdeogram

Initialize the circular layout with an ideogram

Add points to a plotting region

Convert to polar coordinate system

Draw arrow which is paralle to the circle

circos.heatmap.link

Draw a link between two matrix rows in the circular heatmap

circos.genomicPoints

Add points to a plotting region, specifically for genomic graphics

circos.genomicLink

Add links from two sets of genomic positions

Get information of the circular plot

circos.dendrogram

Add circular dendrograms

Make circular heatmaps

circos.updatePlotRegion

Update the plotting region in an existed cell

circos.segments

Draw segments through pairwise of points

Draw text in a cell

circos.genomicAxis

Add genomic axes

circos.genomicLines

Add lines to a plotting region, specifically for genomic graphics

Draw violin plots

circos.genomicLabels

Add labels to specified genomic regions

circos.genomicTrack

Create a track for genomic graphics

Convert unit on x direction in data coordinate

circos.trackPlotRegion

Create plotting regions for a whole track

circos.genomicPosTransformLines

Add genomic position transformation lines between tracks

get.all.track.index

Get index for all tracks

get.cell.meta.data

Get the meta data of a cell

get.current.track.index

Get current track index

Transform back from colors to values

Draw sectors or rings in a circle

highlight.chromosome

Highlight chromosomes

Mark the value as a degree value

Convert unit on y direction in data coordinate

circos.heatmap.initialize

Initialize circular heatmaps

circos.triangle

Convert unit on x direction in data coordinate

get.current.chromosome

Get current chromosome name

circos.genomicTrackPlotRegion

Create a track for genomic graphics

Which data that panel.fun is using

get.current.sector.index

Get current sector index

Add raster images

Draw rectangle-like grid

circos.genomicRainfall

Genomic rainfall plot

Label the sector index and the track index on each cell

Convert unit on x direction in data coordinate

Adjust positions of text

Convert unit on x direction in data coordinate

Convert unit on y direction in data coordinate

posTransform.default

Genomic position transformation function

Nested zooming with two circular plots

names.CELL_META

Names of all meta data in the current cell

Convert unit on y direction in data coordinate

posTransform.text

Genomic position transformation function specifically for text

get.all.sector.index

Get index for all sectors

Create plotting regions for a whole track

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

Calculate genomic region density

Convert unit on y direction in data coordinate

highlight.sector

Highlight sectors and tracks

reverse.circlize

Convert to data coordinate system

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

Convert unit on x direction in data coordinate

print.CELL_META

Print CELL_META

rainfallTransform

Calculate inter-distance of genomic regions

Convert unit on y direction in data coordinate

set.current.cell

Set flag to current cell

Set gaps between tracks

Color interpolation

circos.trackText

Draw text in cells among the whole track

Parameters for the circular layout

circos.trackPoints

Add points to the plotting regions in a same track

generateRandomBed

Generate random genomic data

Convert unit on y direction in data coordinate

Convert fontsize to cex

Generate random colors

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

Convert unit on x direction in data coordinate