All functions

CELL_META

Easy way to get meta data in the current cell

`$`(<CELL_META>)

Easy to way to get meta data in the current cell

add_transparency()

Add transparency to colors

adjacencyList2Matrix()

Convert adjacency list to an adjacency matrix

adjacencyMatrix2List()

Convert adjacency matrix to an adjacency list

calc_gap()

Calculate gaps to make two Chord diagrams in the same scale

chordDiagram()

Plot Chord Diagram

chordDiagramFromDataFrame()

Plot Chord Diagram from a data frame

chordDiagramFromMatrix()

Plot Chord Diagram from an adjacency matrix

circlize-package

Circular visualization in R

circlize()

Convert to polar coordinate system

circos.arrow()

Draw arrow which is paralle to the circle

circos.axis()

Draw x-axis

circos.barplot()

Draw barplots

circos.boxplot()

Draw boxplots

circos.clear()

Reset the circular layout parameters

circos.dendrogram()

Add circular dendrograms

circos.genomicAxis()

Add genomic axes

circos.genomicDensity()

Calculate and add genomic density track

circos.genomicHeatmap()

Add heatmaps for selected regions

circos.genomicIdeogram()

Add an ideogram track

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.genomicLink()

Add links from two sets of genomic positions

circos.genomicPoints()

Add points to a plotting region, specifically for genomic graphics

circos.genomicPosTransformLines()

Add genomic position transformation lines between tracks

circos.genomicRainfall()

Genomic rainfall plot

circos.genomicRect()

Draw rectangle-like grid, specifically for genomic graphics

circos.genomicText()

Draw text in a cell, specifically for genomic graphics

circos.genomicTrack()

Create a track for genomic graphics

circos.genomicTrackPlotRegion()

Create a track for genomic graphics

circos.heatmap()

Make circular heatmaps

circos.heatmap.initialize()

Initialize circular heatmaps

circos.heatmap.link()

Draw a link between two matrix rows in the circular heatmap

circos.info()

Get information of the circular plot

circos.initialize()

Initialize the circular layout

circos.initializeWithIdeogram()

Initialize the circular layout with an ideogram

circos.lines()

Add lines to the plotting region

circos.link()

Draw links between points or/and intervals

circos.nested()

Nested zooming with two circular plots

circos.par()

Parameters for the circular layout

circos.points()

Add points to a plotting region

circos.polygon()

Draw polygon

circos.raster()

Add raster images

circos.rect()

Draw rectangle-like grid

circos.segments()

Draw segments through pairwise of points

circos.text()

Draw text in a cell

circos.track()

Create plotting regions for a whole track

circos.trackHist()

Draw histogram in cells among a whole track

circos.trackLines()

Add lines to the plotting regions in a same track

circos.trackPlotRegion()

Create plotting regions for a whole track

circos.trackPoints()

Add points to the plotting regions in a same track

circos.trackText()

Draw text in cells among the whole track

circos.triangle()

Draw triangles

circos.update()

Create plotting regions for a whole track

circos.updatePlotRegion()

Update the plotting region in an existed cell

circos.violin()

Draw violin plots

circos.xaxis()

Draw x-axis

circos.yaxis()

Draw y-axis

cm_h()

Convert units

cm_x()

Convert unit on x direction in data coordinate

cm_y()

Convert unit on y direction in data coordinate

col2value()

Transform back from colors to values

colorRamp2()

Color interpolation

convert_height()

Convert units

convert_length()

Convert units

convert_x()

Convert unit on x direction in data coordinate

convert_y()

Convert unit on y direction in data coordinate

cytoband.col()

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

degree()

Mark the value as a degree value

draw.sector()

Draw sectors or rings in a circle

fontsize()

Convert fontsize to cex

generateRandomBed()

Generate random genomic data

genomicDensity()

Calculate genomic region density

get.all.sector.index()

Get index for all sectors

get.all.track.index()

Get index for all tracks

get.cell.meta.data()

Get the meta data of a cell

get.current.chromosome()

Get current chromosome name

get.current.sector.index()

Get current sector index

get.current.track.index()

Get current track index

getI()

Which data that panel.fun is using

highlight.chromosome()

Highlight chromosomes

highlight.sector()

Highlight sectors and tracks

inch_h()

Convert units

inch_x()

Convert unit on x direction in data coordinate

inch_y()

Convert unit on y direction in data coordinate

inches_h()

Convert units

inches_x()

Convert unit on x direction in data coordinate

inches_y()

Convert unit on y direction in data coordinate

mm_h()

Convert units

mm_x()

Convert unit on x direction in data coordinate

mm_y()

Convert unit on y direction in data coordinate

names(<CELL_META>)

Names of all meta data in the current cell

posTransform.default()

Genomic position transformation function

posTransform.text()

Genomic position transformation function specifically for text

print(<CELL_META>)

Print CELL_META

rainfallTransform()

Calculate inter-distance of genomic regions

rand_color()

Generate random colors

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

reverse.circlize()

Convert to data coordinate system

set.current.cell()

Set flag to current cell

set_track_gap()

Set gaps between tracks

show.index()

Label the sector index and the track index on each cell

smartAlign()

Adjust positions of text

uh()

Convert units

ux()

Convert unit on x direction in data coordinate

uy()

Convert unit on y direction in data coordinate