R: Circular Visualization

# Circular Visualization

## Documentation for package ‘circlize’ version 0.4.18

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A C D F G H I M N P R S U misc

circlize-package | Circular visualization in R

## -- A --

add_transparency | Add transparency to colors
adjacencyList2Matrix | Convert adjacency list to an adjacency matrix
adjacencyMatrix2List | Convert adjacency matrix to an adjacency list
arrange_links_evenly | Arrange links evenly on each sector

## -- C --

calc_gap | Calculate gaps to make two Chord diagrams in the same scale
CELL_META | Easy way to get meta data in the current cell
chordDiagram | Plot Chord Diagram
chordDiagramFromDataFrame | Plot Chord Diagram from a data frame
chordDiagramFromMatrix | Plot Chord Diagram from an adjacency matrix
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.connect | Draw connecting lines/ribons between two sets of points
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.initializeCircularGenome | Initialize a layout for circular genome
circos.initializeWithIdeogram | Initialize the circular layout with an ideogram
circos.labels | Add a label track
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

## -- D --

degree | Mark the value as a degree value
draw.sector | Draw sectors or rings in a circle

## -- F --

fontsize | Convert fontsize to cex

## -- G --

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
get_most_inside_radius | Get the inside radius of the most inner track

## -- H --

highlight.chromosome | Highlight chromosomes
highlight.sector | Highlight sectors and tracks

## -- I --

inches_h | Convert units
inches_x | Convert unit on x direction in data coordinate
inches_y | Convert unit on y direction in data coordinate
inch_h | Convert units
inch_x | Convert unit on x direction in data coordinate
inch_y | Convert unit on y direction in data coordinate

## -- M --

mm_h | Convert units
mm_x | Convert unit on x direction in data coordinate
mm_y | Convert unit on y direction in data coordinate

## -- N --

names.CELL_META | Names of all meta data in the current cell

## -- P --

posTransform.default | Genomic position transformation function
posTransform.text | Genomic position transformation function specifically for text
print.CELL_META | Print CELL_META

## -- R --

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

## -- S --

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

## -- U --

uh | Convert units
ux | Convert unit on x direction in data coordinate
uy | Convert unit on y direction in data coordinate

## -- misc --

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