A C D F G H I M N P R S U misc
| circlize-package | Circular visualization in R | 
| 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 | 
| 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.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 | 
| 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 | 
| 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 | 
| Subset.CELL_META | Easy to way to get meta data in the current cell | 
| uh | Convert units | 
| ux | Convert unit on x direction in data coordinate | 
| uy | Convert unit on y direction in data coordinate | 
| $.CELL_META | Easy to way to get meta data in the current cell |