I'm trying to use gggenomes to visualize my multiple genome comparison result, and draw a plot showing connection between the homologous genes among 9 genomes and describe the synteny structure. However, I found for some genes, the connection result is not like expectation.
For example, exosc8 in this plot shows two different patterns. For some genomes pair, the linking polygon is well structured, like connecting the end-to-end and start-to-start. However, for the same genes, it makes a bowtie shape (connecting start point to end point). I already checked the strand information and start point / end point information in my links object, but I cannot find any problem. alg5 , smad9 and sparta also show the same problem. One point is, the track set is constant.
There are two groups of track, CC11 to HP6 (group 1) and PJ10 to ST6 (group2).
For the genes show normal connection pattern in group 1 show bowtie shape in group 2 and vice versa.
I really want to know what makes this kind of odd result, and how can I solve this problem. Thank you.
I'm trying to use gggenomes to visualize my multiple genome comparison result, and draw a plot showing connection between the homologous genes among 9 genomes and describe the synteny structure. However, I found for some genes, the connection result is not like expectation.
For example, exosc8 in this plot shows two different patterns. For some genomes pair, the linking polygon is well structured, like connecting the end-to-end and start-to-start. However, for the same genes, it makes a bowtie shape (connecting start point to end point). I already checked the strand information and start point / end point information in my links object, but I cannot find any problem. alg5 , smad9 and sparta also show the same problem. One point is, the track set is constant.
There are two groups of track, CC11 to HP6 (group 1) and PJ10 to ST6 (group2).
For the genes show normal connection pattern in group 1 show bowtie shape in group 2 and vice versa.
I really want to know what makes this kind of odd result, and how can I solve this problem. Thank you.