circos.genomicLink: Add links from two sets of genomic positions

In circlize: Circular Visualization

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()

circlize documentation built on May 29, 2024, 1:59 a.m.