RCircos (version 1.2.2)

RCircos.Vertical.Line.Plot: Draw Vertical Lines on One Data Track

Description

Plot vertical lines on a data track for each genomic position without track outlines and sub-track lines. RCircos core components and graphic devices must be initialized first.

Usage

RCircos.Vertical.Line.Plot(line.data=NULL, track.num=NULL, 
    side=c("in", "out"), line.width=1, inside.pos=NULL,
    outside.pos=NULL, genomic.columns=3, is.sorted=TRUE)

Arguments

line.data

A data frame with leading columns as chromosome names, start position and/or end position of each data point followed by data values for one or more samples.

track.num

Non-negative integer, representing the ordinal number of the plot track where the lines will be plotted.

side

Character vector, either "in" or "out", representing the position related to chromosome ideogram.

line.width

Non-negative integer, width of vertical lines

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.

Examples

# NOT RUN {
library(RCircos);
data(UCSC.HG19.Human.CytoBandIdeogram);
data(RCircos.Line.Data);

RCircos.Set.Core.Components(
    cyto.info=UCSC.HG19.Human.CytoBandIdeogram, 
    chr.exclude=c("chrX", "chrY"), 
    tracks.inside=10, tracks.outside=5) 
RCircos.Set.Plot.Area();
RCircos.Chromosome.Ideogram.Plot()

RCircos.Vertical.Line.Plot(RCircos.Line.Data, track.num=1, side="in")
RCircos.Vertical.Line.Plot(RCircos.Line.Data, side="in", 
    inside.pos=1.5, outside.pos=1.75)
# }