R: Calcualte Plot Positions for A Genomic Interval

RCircos.Get.Paired.Points.Positions {RCircos} | R Documentation

## Calcualte Plot Positions for A Genomic Interval

### Description

Calculate x and y coordinates for a genomic interval which needs two plot positions (start and end) such as link lines/ribbons, tiles, parallel lines. As a set of points for a circlar line is held in the RCircos session, we only need the index of the point for each genomic position.

### Usage

    RCircos.Get.Paired.Points.Positions(genomic.data=NULL, genomic.columns=3,
        plot.type=c("link", "ribbon", "pLink", "polygon", "tile"))

### Arguments

`genomic.data` | A data frame contains paired genomic positions (chromosome names, start and end positions). The data does not need to be sorted.
`genomic.columns` | Non-negative integer, total number of columns for genomic position (chromosome name, start and/or end position).
`plot.type` | Chraracter vector, either "link", "ribbon", "pLink", "polygon", or "tile".

### Value

A data frame same as input but with two new columns for index of plot positions on circular line.

### Author(s)

Henry Zhang

### Examples

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

    RCircos.Set.Core.Components(UCSC.HG19.Human.CytoBandIdeogram,
        chr.exclude=NULL, track.inside=10, tracks.outside=0)
    linkData<-RCircos.Get.Paired.Points.Positions(RCircos.Link.Data,
        genomic.columns=3, plot.type="link")

    ## End(Not run)

[Package RCircos version 1.2.0 Index]