RCircos.Link.Plot: Draw Link Lines between Two or More Genomic Positions

In RCircos: Circos 2D Track Plot

Draw Link Lines between Two or More Genomic Positions

Description

Draw lines (quandratic Bezier curves) between paired genomic positions. RCircos core components and graphic device must be initialize before drawing. Link lines are always in the center of plot area.

Usage

RCircos.Link.Plot(link.data=NULL, track.num=NULL,
    by.chromosome=FALSE, start.pos=NULL, genomic.columns=3,
    is.sorted=TRUE, lineWidth=rep(1, nrow(link.data)))

Arguments

link.data	A data frame with paired genomic positions in each row. The two sets of genomic positions must have same number of columns, e.g., chromosome names, start and end positions or only chromosome names and start positions.
track.num	Non-negative integer, representing the ordinal number of the plot track where the link lines will start.
by.chromosome	Logic. If true, red color will be used for links between positions of same chromosomes and blue color for links between different chromosomes. Otherwise, user defined or random colors (rainbow) will be automatically assigned for each line.
start.pos	Non-negative numeric, scale factor relative to chromosome ideogram position. Must be smaller than 1.
genomic.columns	Non-negative integer, total number of columns for genomic position in each row. Must be either 3 or 2.
is.sorted	Logic, whether the data is sorted by chromosome names and start positions.
lineWidth	Non-negative integer vector, width for each link line.

Author(s)

Henry Zhang

Examples

## Not run: 
library(RCircos);
data(UCSC.HG19.Human.CytoBandIdeogram);
data(RCircos.Link.Data);

RCircos.Set.Core.Components(
	cyto.inf=UCSC.HG19.Human.CytoBandIdeogram,  
	chr.exclude=c("chrX", "chrY"), 
	num.inside=10, num.outside=0)

RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()
RCircos.Link.Plot(RCircos.Link.Data, track.num=4,
	by.chromosome=TRUE)
RCircos.Link.Plot(RCircos.Link.Data, start.pos=0.75,
	by.chromosome=TRUE)

## End(Not run)

RCircos documentation built on March 18, 2022, 7:59 p.m.