How can I solve this error to visualize the gene fusion using the circlize package?

Question

I want to visualize several gene fusions in a circle using the circlize package in R.

My data is

fusion1 <- data.frame("chr" = c("chr7", "chr1", "chr12", "chr3", "chr16", "chr7", "chr12", "chr1"),
                   "start" = c(27934839, 92327028, 24366277, 64430159, 85391249, 27934839, 67462830, 741179),
                   "end" = c(28934839, 93327028, 25366277, 65430159, 86391249, 28934839, 68462830, 1741179))

fusion2 <- data.frame("chr" = c("chr17", "chr1",  "chr12", "chr3",  "chr16", "chr17", "chr12", "chr7"),
                     "start" = c(30267305, 92456741, 24048958, 64184643, 85667520, 30274636, 66990707, 55863785),
                     "end" = c(31267305,93456741, 25048958, 65184643, 86667520, 31274636, 67990707, 56863785))

My code is

library(circlize)
circos.initializeWithIdeogram()
circos.genomicLink(fusion1, fusion2, col = "red", border = NA)
circos.clear()

But I conducted the codes and got an error:

Error in region1[i, 2] == region1[i, 3] : 
  comparison of these types is not implemented

This is what I expacted to happen.

Answer 1

When I run your code, there is no error. Make sure you have a clean environment and make sure your columns have the same types like this:

library(circlize)
circos.initializeWithIdeogram()
circos.genomicLink(fusion1, fusion2, col = "red", border = NA)

circos.clear()

^{Created on 2023-03-04 with reprex v2.0.2}