R: Highlight chromosomes

highlight.chromosome {circlize} | R Documentation

## Highlight chromosomes

### Description

Highlight chromosomes

### Usage

    highlight.chromosome(...)

### Arguments

`...` | pass to `highlight.sector`

### Details

This is only a shortcut function of `highlight.sector`.

### References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

### Examples

    ## Not run:

    par(mar = c(1.5, 1.5, 1.5, 1.5))
    # highlight
    circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
    circos.initializeWithIdeogram(plotType = c("axis", "labels"))

    bed = generateRandomBed(nr = 100)
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
    })

    bed = generateRandomBed(nr = 100)
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
    })

    bed = generateRandomBed(nr = 100)
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
    })

    bed = generateRandomBed(nr = 100)
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicPoints(region, value, pch = 16, cex = 0.5, ...)
    })

    highlight.chromosome("chr1", col = "#FF000040", padding = c(0.05, 0.05, 0.15, 0.05))
    highlight.chromosome("chr3", col = NA, border = "red", lwd = 2,
        padding = c(0.05, 0.05, 0.15, 0.05))
    highlight.chromosome("chr5", col = "#0000FF40", track.index = c(2, 4, 5))
    highlight.chromosome("chr7", col = NA, border = "green", lwd = 2,
        track.index = c(2, 4, 5))
    circos.clear()

    ## End(Not run)

[Package circlize version 0.4.1 Index]