$.CELL_META Easy to way to get meta data in the current cell CELL_META Easy way to get meta data in the current cell 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 calc_gap Calculate gaps to make two Chord diagrams in the same scale 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 circlize-package Circular visualization in R 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 degree Mark the value as a degree value draw.sector Draw sectors or rings in a circle fontsize Convert fontsize to cex 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 highlight.chromosome Highlight chromosomes highlight.sector Highlight sectors and tracks inch_h Convert units inch_x Convert unit on x direction in data coordinate inch_y Convert unit on y direction in data coordinate inches_h Convert units inches_x Convert unit on x direction in data coordinate inches_y Convert unit on y direction in data coordinate mm_h Convert units mm_x Convert unit on x direction in data coordinate mm_y Convert unit on y direction in data coordinate names.CELL_META Names of all meta data in the current cell posTransform.default Genomic position transformation function posTransform.text Genomic position transformation function specifically for text print.CELL_META Print CELL_META 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 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 uh Convert units ux Convert unit on x direction in data coordinate uy Convert unit on y direction in data coordinate