ccGenomicLink: Add links between two sets of genomic positions

In circlizePlus: Using 'ggplot2' Feature to Write Readable R Code for Circular Visualization

Add links between two sets of genomic positions

Description

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

Usage

ccGenomicLink(
  region1,
  region2,
  rou = NULL,
  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

circlizePlus documentation built on June 8, 2025, 10:42 a.m.