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