RCircos.Gene.Name.Plot {RCircos}

Draw Gene Names on a Data Track

Description

Label gene names along chromosome ideogram or a data track. RCircos core components and graphic device must be initialized before drawing.

Usage

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

Arguments

gene.data

A data frame. The first three columns should be chromosome name, start position, end position.

name.col

Non-negative integer, representing the ordinal number of the column in input data that contains gene names.

track.num

Non-negative integer, representing the ordinal number of the plot track where the gene names 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(UCSC.HG19.Human.CytoBandIdeogram)
data(RCircos.Gene.Label.Data)

cyto.info <- UCSC.HG19.Human.CytoBandIdeogram
RCircos.Set.Core.Components(cyto.info,  
    chr.exclude=c("chrX", "chrY"),  
    num.inside=10, num.outside=0)

RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()

gene.data <- RCircos.Gene.Label.Data;
RCircos.Gene.Name.Plot(gene.data, name.col=4,  
    track.num=2, side="in")
RCircos.Gene.Name.Plot(gene.data, name.col=4,  
    track.num=2, side="out",  
    inside.pos=2.5, outside.pos=3)

## End(Not run)