R: Add links from two sets of genomic positions

circos.genomicLink {circlize}

R Documentation

Add links from two sets of genomic positions

Description

Add links from two sets of genomic positions

Usage

circos.genomicLink(region1, region2,
    rou = get_most_inside_radius(), rou1 = rou, rou2 = rou,
    col = "black", lwd = par("lwd"), lty = par("lty"), border = col, ...)

Arguments

`region1`	A genomic data frame
`region2`	A genomic data frame
`rou`	Pass to `circos.link`
`rou1`	Pass to `circos.link`
`rou2`	Pass to `circos.link`
`col`	Pass to `circos.link`, length can be either one or nrow of `region1`
`lwd`	Pass to `circos.link`, length can be either one or nrow of `region1`
`lty`	Pass to `circos.link`, length can be either one or nrow of `region1`
`border`	Pass to `circos.link`, length can be either one or nrow of `region1`
`...`	Pass to `circos.link`

Details

Of course, number of rows should be same in region1 and region2.

If you want to have more controls on links, please use circos.link directly.

References

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

Examples

## Not run: 
set.seed(123)

bed1 = generateRandomBed(nr = 100)
bed1 = bed1[sample(nrow(bed1), 20), ]
bed2 = generateRandomBed(nr = 100)
bed2 = bed2[sample(nrow(bed2), 20), ]
circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
circos.initializeWithIdeogram()

circos.genomicLink(bed1, bed2, col = sample(1:5, 20, replace = TRUE), border = NA)
circos.clear()


## End(Not run)

[Package circlize version 0.4.4 Index]