RCircos.Gene.Connector.Plot {RCircos}

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)