Circular Visualization
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Documentation for package ‘circlize’ version 0.4.16
- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.
Help Pages
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.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 |
-- 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 |