R: Draw Lines between Two Genomic Positions on Same Chromosome

RCircos.Parallel.Line.Plot {RCircos} | R Documentation

## 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)

[Package RCircos version 1.2.0 Index]