RCircos (version 1.2.1)

RCircos.Parallel.Line.Plot: Draw Lines between Two Genomic Positions on Same Chromosome

Description

Plot link lines inside a data track between two genomic positions on same chromosome. RCircos core components and graphic device must be initialized first.

Usage

RCircos.Parallel.Line.Plot(line.data=NULL, track.num=NULL, 
    side=c("in", "out"), line.width=1, inside.pos=NULL,
    outside.pos=NULL, genomic.columns=3, is.sorted=TRUE)

Arguments

line.data

A data frame containing chromosome, start and end position for each line.

track.num

Non-negative integer, the number of track to plot

side

Character vector, relative location to ideogram, either "in" or "out".

line.width

Non-negative numeric, same as lwd in graphic package

inside.pos

Non-negative numeric, inside position (relative to the centre of plot area) of the track.

outside.pos

Non-negative numeric, outside position (relative to the centre of plot area) of the track.

genomic.columns

Non-negative integer, total number of columns for genomic position in each row. Must be 3.

is.sorted

Logic, whether the data is sorted by chromosome names and start positions.

Examples

# NOT RUN {
library(RCircos);
data(UCSC.HG19.Human.CytoBandIdeogram);
data(RCircos.Line.Data);

RCircos.Set.Core.Components(
    cyto.info=UCSC.HG19.Human.CytoBandIdeogram, 
    chr.exclude=c("chrX", "chrY"), 
    tracks.inside=10, tracks.outside=5) 
RCircos.Set.Plot.Area();
RCircos.Chromosome.Ideogram.Plot()

RCircos.Parallel.Line.Plot(line.data, track.num=5, side="in")
RCircos.Parallel.Line.Plot(line.data, line.width=2, 
    inside.pos=2, outside.pos=2.5)
# }