Man pages for circlize
Circular Visualization

add_transparencyAdd transparency to colors
adjacencyList2MatrixConvert adjacency list to an adjacency matrix
adjacencyMatrix2ListConvert adjacency matrix to an adjacency list
arrange_links_evenlyArrange links evenly on each sector
calc_gapCalculate gaps to make two Chord diagrams in the same scale
CELL_METAEasy way to get meta data in the current cell
chordDiagramPlot Chord Diagram
chordDiagramFromDataFramePlot Chord Diagram from a data frame
chordDiagramFromMatrixPlot Chord Diagram from an adjacency matrix
circlizeConvert to polar coordinate system
circlize-packageCircular visualization in R
circos.arrowDraw arrow which is paralle to the circle
circos.axisDraw x-axis
circos.barplotDraw barplots
circos.boxplotDraw boxplots
circos.clearReset the circular layout parameters
circos.connectDraw connecting lines/ribons between two sets of points
circos.dendrogramAdd circular dendrograms
circos.genomicAxisAdd genomic axes
circos.genomicDensityCalculate and add genomic density track
circos.genomicHeatmapAdd heatmaps for selected regions
circos.genomicIdeogramAdd an ideogram track
circos.genomicInitializeInitialize circular plot with any genomic data
circos.genomicLabelsAdd labels to specified genomic regions
circos.genomicLinesAdd lines to a plotting region, specifically for genomic...
circos.genomicLinkAdd links from two sets of genomic positions
circos.genomicPointsAdd points to a plotting region, specifically for genomic...
circos.genomicPosTransformLinesAdd genomic position transformation lines between tracks
circos.genomicRainfallGenomic rainfall plot
circos.genomicRectDraw rectangle-like grid, specifically for genomic graphics
circos.genomicTextDraw text in a cell, specifically for genomic graphics
circos.genomicTrackCreate a track for genomic graphics
circos.genomicTrackPlotRegionCreate a track for genomic graphics
circos.heatmapMake circular heatmaps
circos.heatmap.initializeInitialize circular heatmaps
circos.heatmap.linkDraw a link between two matrix rows in the circular heatmap
circos.infoGet information of the circular plot
circos.initializeInitialize the circular layout
circos.initializeCircularGenomeInitialize a layout for circular genome
circos.initializeWithIdeogramInitialize the circular layout with an ideogram
circos.labelsAdd a label track
circos.linesAdd lines to the plotting region
circos.linkDraw links between points or/and intervals
circos.nestedNested zooming with two circular plots
circos.parParameters for the circular layout
circos.pointsAdd points to a plotting region
circos.polygonDraw polygon
circos.rasterAdd raster images
circos.rectDraw rectangle-like grid
circos.segmentsDraw segments through pairwise of points
circos.textDraw text in a cell
circos.trackCreate plotting regions for a whole track
circos.trackHistDraw histogram in cells among a whole track
circos.trackLinesAdd lines to the plotting regions in a same track
circos.trackPlotRegionCreate plotting regions for a whole track
circos.trackPointsAdd points to the plotting regions in a same track
circos.trackTextDraw text in cells among the whole track
circos.triangleDraw triangles
circos.updateCreate plotting regions for a whole track
circos.updatePlotRegionUpdate the plotting region in an existed cell
circos.violinDraw violin plots
circos.xaxisDraw x-axis
circos.yaxisDraw y-axis
cm_hConvert units
cm_xConvert unit on x direction in data coordinate
cm_yConvert unit on y direction in data coordinate
col2valueTransform back from colors to values
colorRamp2Color interpolation
convert_heightConvert units
convert_lengthConvert units
convert_xConvert unit on x direction in data coordinate
convert_yConvert unit on y direction in data coordinate
cytoband.colAssign colors to cytogenetic band (hg19) according to the...
degreeMark the value as a degree value
draw.sectorDraw sectors or rings in a circle
fontsizeConvert fontsize to cex
generateRandomBedGenerate random genomic data
genomicDensityCalculate genomic region density
get.all.sector.indexGet index for all sectors
get.all.track.indexGet index for all tracks
get.cell.meta.dataGet the meta data of a cell
get.current.chromosomeGet current chromosome name
get.current.sector.indexGet current sector index
get.current.track.indexGet current track index
getIWhich data that '' is using
get_most_inside_radiusGet the inside radius of the most inner track
highlight.chromosomeHighlight chromosomes
highlight.sectorHighlight sectors and tracks
inches_hConvert units
inches_xConvert unit on x direction in data coordinate
inches_yConvert unit on y direction in data coordinate
inch_hConvert units
inch_xConvert unit on x direction in data coordinate
inch_yConvert unit on y direction in data coordinate
mm_hConvert units
mm_xConvert unit on x direction in data coordinate
mm_yConvert unit on y direction in data coordinate
names.CELL_METANames of all meta data in the current cell
posTransform.defaultGenomic position transformation function
posTransform.textGenomic position transformation function specifically for...
rainfallTransformCalculate inter-distance of genomic regions
rand_colorGenerate random colors
read.chromInfoRead/parse chromInfo data from a data frame/file/UCSC...
read.cytobandRead/parse cytoband data from a data frame/file/UCSC database
reverse.circlizeConvert to data coordinate system
set.current.cellSet flag to current cell
set_track_gapSet gaps between tracks
show.indexLabel the sector index and the track index on each cell
smartAlignAdjust positions of text
Subset.CELL_METAEasy to way to get meta data in the current cell
uhConvert units
uxConvert unit on x direction in data coordinate
uyConvert unit on y direction in data coordinate
circlize documentation built on May 11, 2022, 1:06 a.m.