Add links between two sets of genomic positions

Object ccGenomicLink will call the function circlize::circos.genomicLink while drawing.

Usage

ccGenomicLink(
  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.

Value

Object ccGenomicLink

Examples

library(circlizePlus)
set.seed(123)

bed1 = generateRandomBed(nr = 100)
bed1 = bed1[sample(nrow(bed1), 20), ]
bed2 = generateRandomBed(nr = 100)
bed2 = bed2[sample(nrow(bed2), 20), ]
par1 = ccPar("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
cc = ccPlot(initMode="initializeWithIdeogram")

link1 = ccGenomicLink(bed1, bed2, col = sample(1:5, 20, replace = TRUE), border = NA)
cc + par1 + link1