R: Draw Connectors between Chromosome Ideogram and Gene Names

RCircos.Gene.Connector.Plot {RCircos} | R Documentation

## Draw Connectors between Chromosome Ideogram and Gene Names

### Description

Draw a set of connectors (three lines for each connector) between chromosome ideogram or a data track and gene names. RCircos core components and graphics device must be initialized before drawing.

### Usage

    RCircos.Gene.Connector.Plot(genomic.data=NULL, track.num=NULL,
            side="in", inside.pos=NULL, outside.pos=NULL,
            genomic.columns=3, is.sorted=FALSE)

### Arguments

`genomic.data` | A data frame with the first four columns for chromosome names, start positions, end positions, and gene names.
`track.num` | Non-negative integer, representing the ordinal number of the plot track where the connectors are plotted.
`side` | Character vector, either "in" or "out" representing the position related to chromosome ideogram.
`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 either 3 or 2.
`is.sorted` | Logic, whether the data is sorted by chromosome names and start positions.

### Author(s)

Henry Zhang

### Examples

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

    cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
    RCircos.Set.Core.Components(cyto.info, chr.exclude=NULL,
           tracks.inside=10, tracks.outside=0)

    gene.data <- RCircos.Gene.Label.Data
    RCircos.Set.Plot.Area()
    RCircos.Chromosome.Ideogram.Plot()
    RCircos.Gene.Connector.Plot(gene.data, track.num=1, side="in")
    RCircos.Gene.Connector.Plot(gene.data, side="out",
        inside.pos=2.5, outside.pos=3)

    ## End(Not run)

[Package RCircos version 1.2.0 Index]