R: Plot A Customized Shape

RCircos.Customized.Shape.Plot {RCircos} | R Documentation

## 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)

[Package RCircos version 1.2.0 Index]