Learn R Programming

⚠️There's a newer version (0.4.16) of this package.Take me there.

circlize (version 0.4.1)

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.

Copy Link

Version

Install

install.packages('circlize')

Monthly Downloads

34,353

Version

0.4.1

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Maintainer

Last Published

July 19th, 2017

Functions in circlize (0.4.1)

add_transparency

Add transparency to colors
adjacencyList2Matrix

Convert adjacency list to adjacency matrix
circos.genomicLink

Add links from two sets of genomic positions
circos.genomicPoints

Add points to a plotting region, specifically for genomic graphics
circos.genomicTrack

Create a track for genomic graphics
circos.genomicTrackPlotRegion

Create a track for genomic graphics
circos.par

Parameters for the circular layout
circos.points

Add points to a plotting region
colorRamp2

Color interpolation
convert_height

Convert units
convert_y

Convert unit on y direction in data coordinate
cytoband.col

Assign colors to cytogenetic band (hg19) according to the Giemsa stain results
get.current.sector.index

Get current sector index
get.current.track.index

Get current track index
reverse.circlize

Convert to data coordinate system
set.current.cell

Set flag to current cell
CELL_META

Easy to way to get meta data in the current cell
$.CELL_META

Easy to way to get meta data in the current cell
circos.genomicLabels

Add labels to specified genomic regions
circos.genomicLines

Add lines to a plotting region, specifically for genomic graphics
circos.initializeWithIdeogram

Initialize the circular layout with an ideogram
circos.lines

Add lines to the plotting region
circos.text

Draw text in a cell
circos.track

Create plotting regions for a whole track
circos.trackPlotRegion

Create plotting regions for a whole track
circos.trackPoints

Add points to the plotting regions in a same track
generateRandomBed

Generate random genomic data
genomicDensity

Calculate genomic region density
getI

Which data that panel.fun is using
highlight.chromosome

Highlight chromosomes
uh

Convert units
ux

Convert unit on x direction in data coordinate
uy

Convert unit on y direction in data coordinate
circos.arrow

Draw arrow which is paralle to the circle
circos.axis

Draw x-axis
circos.genomicIdeogram

Add an ideogram track
circos.genomicInitialize

Initialize circular plot with any genomic data
circos.info

Get information of the circular plot
circos.initialize

Initialize the circular layout
circos.polygon

Draw polygon
circos.raster

Add raster images
circos.updatePlotRegion

Update the plotting region in an existed cell
circos.xaxis

Draw x-axis
get.all.sector.index

Get index for all sectors
get.all.track.index

Get index for all tracks
highlight.sector

Highlight sectors and tracks
posTransform.default

Genomic position transformation function
show.index

Label the sector index and the track index on each cell
smartAlign

Adjust positions of text
circos.clear

Reset the circular layout parameters
circos.dendrogram

Add circular dendrograms
circos.genomicDensity

Calculate and add genomic density track
circos.genomicHeatmap

Add heatmaps for selected regions
circos.genomicRect

Draw rectangle-like grid, specifically for genomic graphics
circos.genomicText

Draw text in a cell, specifically for genomic graphics
circos.rect

Draw rectangle-like grid
circos.segments

Draw segments through pairwise of points
circos.trackText

Draw text in cells among the whole track
circos.update

Create plotting regions for a whole track
convert_length

Convert units
convert_x

Convert unit on x direction in data coordinate
posTransform.text

Genomic position transformation function specifically for text
print.CELL_META

Print CELL_META
circlize-package

Circular visualization in R
circlize

Convert to polar coordinate system
rainfallTransform

Calculate inter-distance of genomic regions
rand_color

Generate random colors
circos.genomicPosTransformLines

Add genomic position transformation lines between tracks
circos.genomicRainfall

Genomic rainfall plot
circos.link

Draw links between points or/and intervals
circos.nested

Nested zooming with two circular plots
circos.trackHist

Draw histogram in cells among a whole track
circos.trackLines

Add lines to the plotting regions in a same track
circos.yaxis

Draw y-axis
col2value

Transform back from colors to values
degree

Mark the value as a degree value
draw.sector

Draw sectors or rings in a circle
get.cell.meta.data

Get the meta data of a cell
get.current.chromosome

Get current chromosome name
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