circos.genomicLink {circlize}

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 data frame in bed format.

region2

A data frame in bed format.

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.

See Also

https://jokergoo.github.io/circlize_book/book/genomic-plotting-region.html#genomic-links

Examples

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()