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