RCircos (version 1.2.2)

RCircos.Customized.Shape.Plot: Plot A Customized Shape

Description

Plot one customized shape on a data track. RCircos core components and graphic device must be initialized first. The customized shape should be represented by coordinates of a polygon inside a circle with radius of 1 and default location is at 12 o'clock. When plotting, the polygon center will be scaled and transformed for new size and location. For example, following code will plot an arrow:

polygonX <- c(0, -0.7, -0.2, -0.2, 0.2, 0.2, 0.7, 0) polygonY <- c(-1, 0.7, 0.4, 1, 1, 0.4, 0.7, -1) plot(c(-2, 2), c(-2, 2)) polygon(polygonX, polygonY, col="red")

Usage

RCircos.Customized.Shape.Plot(shape.data=NULL, track.num=NULL,  
    side=c("in", "out"), location=NULL, shape.color="red",
    inside.pos=NULL, outside.pos=NULL)

Arguments

shape.data

A two dimensional numeric matrix for coordinates of a polygon

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.

location

Vector with chromosome name, start position, and end position where the shap to be drawn.

shape.color

Character vector, color for the shape.

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.

Examples

# NOT RUN {
library(RCircos)  

data(UCSC.HG19.Human.CytoBandIdeogram)
RCircos.Set.Core.Components(UCSC.HG19.Human.CytoBandIdeogram,  
    chr.exclude=NULL, tracks.inside=10, tracks.outside=0)

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

shape <- cbind(c(0, -0.7, -0.2, -0.2, 0.2, 0.2, 0.7, 0),  
        c(-1, 0.7,  0.4,  1,   1,   0.4, 0.7, -1))
RCircos.Customized.Shape.Plot(shape, track.num=1, side="in")
# }