Circular Visualization


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Documentation for package ‘circlize’ version 0.3.8

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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