BioCircos (version 0.3.4)

BioCircosSNPTrack: Create a track with SNPs to be added to a BioCircos tracklist

Description

SNPs are defined by genomic coordinates and associated with a numerical value

Usage

BioCircosSNPTrack(trackname, chromosomes, positions, values,
  colors = "#40B9D4", labels = "", size = 2, shape = "circle",
  opacities = 1, maxRadius = 0.9, minRadius = 0.5, range = 0, ...)

Arguments

trackname

The name of the new track.

chromosomes

A vector containing the chromosomes on which each SNP are found. Values should match the chromosome names given in the genome parameter of the BioCircos function.

positions

A vector containing the coordinates on which each SNP are found. Values should be inferior to the chromosome lengths given in the genome parameter of the BioCircos function.

values

A vector of numerical values associated with each SNPs, used to determine the radial coordinates of each point on the visualization.

colors

The colors for each point. Can be a RColorBrewer palette name used to generate one color per point, or a character object or vector of character objects stating RGB values in hexadecimal format or base R colors. If the vector is shorter than the number of points, values will be repeated.

labels

One or multiple character objects to label each point.

size

The size of each point.

shape

Shape of the points. Can be "circle" or "rect".

opacities

One or multiple opacity values for the points, between 0 and 1.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

range

Vector of values to be mapped to the minimum and maximum radii of the track. Default to 0, mapping the minimal and maximal values input in the values parameter.

...

Ignored

Examples

# NOT RUN {
BioCircos(BioCircosSNPTrack('SNPTrack', chromosomes = 1:3, positions = 1e+7*2:4, 
  values = 1:3, colors = "Accent", labels = c('A', 'B', 'C')) + BioCircosBackgroundTrack('BGTrack'))

# }