BioCircos (version 0.3.4)

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

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

# NOT RUN {
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'))

# }