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

In RCircos: Circos 2D Track 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.

Author(s)

Henry Zhang

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")

## End(Not run)

RCircos documentation built on March 18, 2022, 7:59 p.m.