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CELL_META
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Easy way to get meta data in the current cell |
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`$`(<CELL_META>)
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Easy to way to get meta data in the current cell |
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add_transparency()
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Add transparency to colors |
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adjacencyList2Matrix()
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Convert adjacency list to an adjacency matrix |
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adjacencyMatrix2List()
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Convert adjacency matrix to an adjacency list |
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calc_gap()
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Calculate gaps to make two Chord diagrams in the same scale |
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chordDiagram()
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Plot Chord Diagram |
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chordDiagramFromDataFrame()
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Plot Chord Diagram from a data frame |
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chordDiagramFromMatrix()
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Plot Chord Diagram from an adjacency matrix |
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circlize-package
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Circular visualization in R |
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circlize()
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Convert to polar coordinate system |
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circos.arrow()
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Draw arrow which is paralle to the circle |
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circos.axis()
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Draw x-axis |
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circos.barplot()
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Draw barplots |
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circos.boxplot()
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Draw boxplots |
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circos.clear()
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Reset the circular layout parameters |
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circos.dendrogram()
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Add circular dendrograms |
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circos.genomicAxis()
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Add genomic axes |
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circos.genomicDensity()
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Calculate and add genomic density track |
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circos.genomicHeatmap()
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Add heatmaps for selected regions |
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circos.genomicIdeogram()
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Add an ideogram track |
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circos.genomicInitialize()
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Initialize circular plot with any genomic data |
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circos.genomicLabels()
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Add labels to specified genomic regions |
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circos.genomicLines()
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Add lines to a plotting region, specifically for genomic graphics |
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circos.genomicLink()
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Add links from two sets of genomic positions |
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circos.genomicPoints()
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Add points to a plotting region, specifically for genomic graphics |
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circos.genomicPosTransformLines()
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Add genomic position transformation lines between tracks |
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circos.genomicRainfall()
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Genomic rainfall plot |
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circos.genomicRect()
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Draw rectangle-like grid, specifically for genomic graphics |
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circos.genomicText()
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Draw text in a cell, specifically for genomic graphics |
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circos.genomicTrack()
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Create a track for genomic graphics |
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circos.genomicTrackPlotRegion()
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Create a track for genomic graphics |
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circos.heatmap()
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Make circular heatmaps |
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circos.heatmap.initialize()
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Initialize circular heatmaps |
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circos.heatmap.link()
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Draw a link between two matrix rows in the circular heatmap |
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circos.info()
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Get information of the circular plot |
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circos.initialize()
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Initialize the circular layout |
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circos.initializeWithIdeogram()
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Initialize the circular layout with an ideogram |
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circos.lines()
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Add lines to the plotting region |
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circos.link()
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Draw links between points or/and intervals |
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circos.nested()
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Nested zooming with two circular plots |
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circos.par()
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Parameters for the circular layout |
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circos.points()
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Add points to a plotting region |
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circos.polygon()
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Draw polygon |
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circos.raster()
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Add raster images |
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circos.rect()
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Draw rectangle-like grid |
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circos.segments()
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Draw segments through pairwise of points |
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circos.text()
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Draw text in a cell |
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circos.track()
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Create plotting regions for a whole track |
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circos.trackHist()
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Draw histogram in cells among a whole track |
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circos.trackLines()
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Add lines to the plotting regions in a same track |
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circos.trackPlotRegion()
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Create plotting regions for a whole track |
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circos.trackPoints()
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Add points to the plotting regions in a same track |
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circos.trackText()
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Draw text in cells among the whole track |
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circos.triangle()
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Draw triangles |
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circos.update()
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Create plotting regions for a whole track |
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circos.updatePlotRegion()
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Update the plotting region in an existed cell |
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circos.violin()
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Draw violin plots |
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circos.xaxis()
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Draw x-axis |
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circos.yaxis()
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Draw y-axis |
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cm_h()
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Convert units |
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cm_x()
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Convert unit on x direction in data coordinate |
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cm_y()
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Convert unit on y direction in data coordinate |
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col2value()
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Transform back from colors to values |
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colorRamp2()
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Color interpolation |
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convert_height()
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Convert units |
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convert_length()
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Convert units |
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convert_x()
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Convert unit on x direction in data coordinate |
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convert_y()
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Convert unit on y direction in data coordinate |
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cytoband.col()
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Assign colors to cytogenetic band (hg19) according to the Giemsa stain results |
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degree()
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Mark the value as a degree value |
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draw.sector()
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Draw sectors or rings in a circle |
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fontsize()
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Convert fontsize to cex |
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generateRandomBed()
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Generate random genomic data |
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genomicDensity()
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Calculate genomic region density |
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get.all.sector.index()
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Get index for all sectors |
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get.all.track.index()
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Get index for all tracks |
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get.cell.meta.data()
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Get the meta data of a cell |
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get.current.chromosome()
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Get current chromosome name |
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get.current.sector.index()
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Get current sector index |
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get.current.track.index()
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Get current track index |
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getI()
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Which data that panel.fun is using |
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highlight.chromosome()
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Highlight chromosomes |
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highlight.sector()
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Highlight sectors and tracks |
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inch_h()
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Convert units |
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inch_x()
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Convert unit on x direction in data coordinate |
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inch_y()
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Convert unit on y direction in data coordinate |
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inches_h()
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Convert units |
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inches_x()
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Convert unit on x direction in data coordinate |
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inches_y()
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Convert unit on y direction in data coordinate |
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mm_h()
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Convert units |
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mm_x()
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Convert unit on x direction in data coordinate |
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mm_y()
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Convert unit on y direction in data coordinate |
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names(<CELL_META>)
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Names of all meta data in the current cell |
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posTransform.default()
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Genomic position transformation function |
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posTransform.text()
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Genomic position transformation function specifically for text |
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print(<CELL_META>)
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Print CELL_META |
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rainfallTransform()
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Calculate inter-distance of genomic regions |
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rand_color()
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Generate random colors |
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read.chromInfo()
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Read/parse chromInfo data from a data frame/file/UCSC database |
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read.cytoband()
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Read/parse cytoband data from a data frame/file/UCSC database |
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reverse.circlize()
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Convert to data coordinate system |
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set.current.cell()
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Set flag to current cell |
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set_track_gap()
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Set gaps between tracks |
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show.index()
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Label the sector index and the track index on each cell |
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smartAlign()
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Adjust positions of text |
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uh()
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Convert units |
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ux()
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Convert unit on x direction in data coordinate |
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uy()
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Convert unit on y direction in data coordinate |