circlize (version 0.4.1)

circos.genomicLink: 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()

# }
# NOT RUN {
# }