RCircos.Parallel.Line.Plot {RCircos}

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.

Author(s)

Henry Zhang

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)

## End(Not run)