RCircos (version 1.2.2)

RCircos.Pseudo.Ideogram.From.Table: Generate Pseudo Chromosome Ideogram from Plot Data Table

Description

Generate a pseudo ideogram from plot data for Circos plot. Plot data must have at least two columns serving as chromosome names and band names. An optional gene length or locations can also be provided, e.g.,

Groups LocusName LocusPosition Group1 1 1.5 Group1 3 2.0 Group1 4 3.0

Usage

RCircos.Pseudo.Ideogram.From.Table(plot.data=NULL, location.col=NULL, band.col=NULL)

Arguments

plot.data

A data frame with two or three columns, the first column is for chromosome names.

location.col

Non negative integer, column number in plot.data from which end positions will be derived for each chromosome or each band. This argument must be defined and could be either length of the locus or relative locus position.

band.col

Non negative integer, column number in plot.data which serves as band names, this argument is optional.

Value

A data frame with ideogram data.

Examples

# NOT RUN {
library(RCircos)
data(RCircos.Gene.Label.Data);
plot.data <- RCircos.Gene.Label.Data;
cyto.info <- RCircos.Get.Pseudo.Ideogram(plot.data=plot.data, 
	location.col=2, band.col=3)
# }