Circular Visualization


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Documentation for package ‘circlize’ version 0.4.13

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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.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