RCircos (version 1.2.1)

RCircos.Set.Core.Components: Initialize Core Components for RCircos Plot

Description

Setup core components for RCircos Plot including plot parameters, cytoband data, and base plot positions. This function must be called before chromosome ideogram and any other data plot.

Usage

RCircos.Set.Core.Components(cyto.info, chr.exclude = NULL, tracks.inside, tracks.outside)

Arguments

cyto.info

A data frame with chromosome ideogram data and columns are ordered by chromosome names, start position, end position, band names, and stain intensity for each chromosome band.

chr.exclude

Character vector of chromosome names to be excluded from plot, e.g., chr.exclude <- c("chrX", "chrY");

tracks.inside

Non-negative integer, total number of data tracks inside of chromosome ideogram to be plotted.

tracks.outside

Non-negative integer, total number of data tracks outside of chromosome ideogram to be plotted.

Examples

# NOT RUN {
library(RCircos)
data(UCSC.HG19.Human.CytoBandIdeogram)
RCircos.Set.Core.Components(
	cyto.info=UCSC.HG19.Human.CytoBandIdeogram, 
	chr.exclude=c("chrX", "chrY"), 
	tracks.inside=10, tracks.outside=0) 
# }