R/Circos, cannot make inter-chromosomal links to multiple chromosomes.

Question

[shenucide]

I'm trying to make a synteny plot using R/Circos.

I have two input files, one file with "cytogenetic" information for all chromosomes in both species.

Chromosome  ChromStart  ChromEnd    Band    Stain
X   1       73195   1A1 gneg
X   73195   86828   1A2 gpos
chr3    28681620    28681643    383 gpos
chr3    28681643    28681652    384 gneg

The second input file has the linkages (every line is a gene, the first three columns are the chromosome, start, and stop in species A and the second three are the chromosome, start, and stop in species B)

Chromosome  chromStart  chromEnd    Chromosome.1    chromStart.1    chromEnd.1
X   143006  147332  chr3    49167572    49168700
X   196281  198758  chr3    48985944    48987075
X   244442  245670  chr3    50638796    50639069
X   246850  253258  chr3    48958829    48960058

I can make the circle of chromosomes fine, and it's all labeled correctly, but when I try to make the links between chromosomes, the program won't allow links happen between one chromosome from species A to two different chromosomes in species B, even when I set by.chromosome=F. In other words, if there are two genes on chromosome x in species A, and they go to two different chromosomes in species B, I get the error:

Error in RCircos.Validate.Genomic.Data(link.data, plot.type = "link") : Location is outside of chromosome length.

I know it has to do with the fact that they're going to two different chromosomes because I manually checked all the boundaries of the chromosomes and all the gene positions are within them.

Does anyone have any ideas or suggestions on how to make multiple inter-chromosomal links using R/Circos?

Thanks!

[user_g]

Hello, I am having the same problem now. Did you manage to make it work?