BioCircosLinkTrack: Create an inner track with links to be added to a BioCircos...

In BioCircos: Interactive Circular Visualization of Genomic Data using 'htmlwidgets' and 'BioCircos.js'

Description

Links are defined by beginning and ending genomic coordinates of the 2 regions to linked, such as the positions linked in genomic fusions.

Usage

BioCircosLinkTrack(trackname, gene1Chromosomes, gene1Starts, gene1Ends,
  gene2Chromosomes, gene2Starts, gene2Ends, color = "#40B9D4",
  labels = "", maxRadius = 0.4, width = "0.1em", gene1Names = "",
  gene2Names = "", displayAxis = TRUE, axisColor = "#B8B8B8",
  axisWidth = 0.5, axisPadding = 0, displayLabel = TRUE,
  labelColor = "#000000", labelSize = "1em", labelPadding = 3, ...)

Arguments

trackname	The name of the new track.
gene1Chromosomes, gene1Starts, gene1Ends, gene1Names, gene2Chromosomes, gene2Starts, gene2Ends, gene2Names	Vectors with the chromosomes, genomic coordinates of beginning and end, and names of both genes to link. Chromosomes and positions should respect the chromosome names and lengths given in the genome parameter of the BioCircos function.
color	The color for the links, in hexadecimal RGB format.
labels	A vector of character objects to label each link.
maxRadius	Where the track should end, in proportion of the inner radius of the plot.
width	The thickness of the links.
displayAxis	Display additional axis (i.e. circle) around the track.
axisColor, axisWidth, axisPadding	Color, thickness and padding of the additional axis.
displayLabel	Display labels of the track.
labelColor, labelSize, labelPadding	Color, font size and padding of the labels around the track.
...	Ignored

Examples

start_chromosomes <- 1:5
end_chromosomes <- 2*10:6
start_pos <- 2.5e+7*2:6
end_pos <- 2e+7*1:5
BioCircos(BioCircosLinkTrack('LinkTrack', start_chromosomes, start_pos, start_pos+1,
  end_chromosomes, end_pos, end_pos+1, color = '#FF00FF'))

BioCircos documentation built on May 2, 2019, 9:42 a.m.