RCircos (version 1.2.2)

RCircos.Reset.Core.Components: Reset Methods for Modifying RCircos Core Components

Description

Reset RCircos core components: plot ideogram, plot position, and plot parameters.

Usage

RCircos.Reset.Plot.Ideogram(chrom.ideo)
RCircos.Reset.Plot.Positions(plot.positions)
RCircos.Reset.Plot.Parameters(new.params)

Arguments

chrom.ideo

Data frame, object of RCircos cytoband data returned from RCircos.Get.Plot.Ideogram().

plot.positions

Data frame, object of RCircos plot positions returned from RCircos.Get.Plot.Positions().

new.params

List, object of RCircos plot positions returned from RCircos.Get.Plot.Parameters()

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=5) 

ideo <- RCircos.Get.Plot.Ideogram()
rows <- which(ideo$BandColor=="red"
ideo$BandColor[rows] <- "green"
RCircos.Reset.Plot.Ideogram(ideo)

params <- RCircos.Get.Plot.Parameters()
params$base.per.unit <- 6000
RCircos.Reset.Plot.Paramters(params)

positions <- RCircos.Get.Plot.Positions();
positions[1, 3] <- 0;
RCircos.Reset.Plot.Positions(positions);
# }