ggbio_plot_loop.R

library(GenomicRanges)
library(ggbio)

pairs.df <- read.table("D:/tmp/ggbio_demo/ZQL-49_final.txt",header=FALSE, sep="\t")[,1:7]
colnames(pairs.df) <- c("read", "chr1", "pos1", "chr2", "pos2", "strand1", "strand2")

chromsize.df <- read.csv("D:/tmp/ggbio_demo/susScr11_ASFV_noun.fa.csv") 

chromsize.gr <- GRanges(
  seqnames = chromsize.df$seqnames,
  ranges = IRanges(start=1, end=chromsize.df$end),
)
seqlengths(chromsize.gr) <- chromsize.df$width


pairs.gr <- GRanges(
  seqnames = pairs.df$chr1,
  ranges = IRanges(start=pairs.df$pos1, end=pairs.df$pos1),
  seqlengths = seqlengths(chromsize.gr),
  to.gr = GRanges(
    seqnames=pairs.df$chr2,
    ranges=IRanges(start=pairs.df$pos2, end=pairs.df$pos2),
    seqlengths = seqlengths(chromsize.gr)),
)


p <- ggbio() +
  circle(chromsize.gr, geom="ideo", fill="gray70") +
  circle(chromsize.gr, geom="scale", size=2) +
  circle(chromsize.gr, geom="text", aes(label=seqnames), vjust=0, size=3) +
  circle(pairs.gr, geom="link", linked.to="to.gr", radius=30, aes(color=seqnames))

p

GRanges object should specify the seqlengths attribute when plot the "link" geom.