RCircos (version 1.2.2)

RCircos.Line.Plot: Draw Lines for One Data Track

Description

Draw one track of continue lines which connect each neighbor data points. RCircos core components and graphics device must bae initialized before drawing.

Usage

RCircos.Line.Plot(line.data=NULL, data.col=4, track.num=NULL,  
    side=c("in", "out"), min.value=NULL, max.value=NULL,  
    inside.pos=NULL, outside.pos=NULL, genomic.columns=3,  
    is.sorted=TRUE)

Arguments

line.data

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

data.col

Non-negative integer, representing the ordinal number of the column in input dataset that contains the data to be plotted.

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.

min.value

Numeric, minimum value of line data.

max.value

Numeric, maximum value of line data

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"),  
    num.inside=10, num.outside=0) 

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

RCircos.Line.Plot(RCircos.Line.Data, data.col=5,  
    track.num=1, side="in")
RCircos.Line.Plot(RCircos.Line.Data, data.col=5,  
    side="in", inside.pos=1.5, outside.pos=1.75)  
# }