# Circular Visualization

## Documentation for package ‘circlize’ version 0.3.9

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

## Help Pages

circlize-package | Circular layout in R
adjacencyList2Matrix | Convert adjacency list to adjacency matrix
chordDiagram | Plot Chord Diagram
chordDiagramFromDataFrame | Plot Chord Diagram from a data frame
chordDiagramFromMatrix | Plot Chord Diagram from a matrix
circlize | Return the coordinate in polar coordinate system
circos.axis | Draw x-axis
circos.clear | Reset the circos layout parameters
circos.dendrogram | Add circlized dendrograms
circos.genomicDensity | Calculate and add genomic density track
circos.genomicInitialize | Initialize circos plot with any genomic data
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.info | Get information of the circos plot
circos.initialize | Initialize the circos layout
circos.initializeWithIdeogram | Initialize the circos layout with an ideogram
circos.lines | Add lines to the plotting region
circos.link | Draw links between points or intervals
circos.par | Parameters for circos layout
circos.points | Add points to a plotting region
circos.polygon | Draw polygon
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.update | Create plotting regions for a whole track
circos.updatePlotRegion | Update the plotting region in an existed cell
circos.xaxis | Draw x-axis
circos.yaxis | Draw y-axis
col2value | Transform colors to values
colorRamp2 | Color interpolation
cytoband.col | Assign colors to cytogenetic band (hg19) according to the Giemsa stain results
degree | mark the value is degree value
draw.sector | Draw sectors or rings in a circle
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
getI | Which data that 'panel.fun' is using
highlight.chromosome | Highlight chromosomes
highlight.sector | Highlight sectors and tracks
posTransform.default | Genomic position transformation function
posTransform.text | Genomic position transformation function specifically for text
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 | Return the coordinate in data coordinate system
show.index | Label the sector index and the track index on each cell
smartAlign | Adjust positions of text