How to draw intra- and interspecies synteny blocks the same time?

[justdx]

Dear Hao, Thanks for the nice tool first. As mentioned in the title, I would like to ask how to draw both intra- and interspecies synteny blocks, such as Figure 1d in the Liriodendron genome paper?

[TickingClock1992]

Hello, thanks for following our research paper. Originally, RIdeogram was developed to plot this figure. However, it is a little bit difficult to merge all the functions into the R package RIdeogram. If you want to draw the intra- and interspecies synteny blocks the same time, I can sent the original script that I used to plot this figure. Leave me your e-mail address.

[justdx]

My email address is justdx0713@gmail.com, thanks a lot for your help.

[TickingClock1992]

No problem！

[evolgen]

Hi Hao,

Is there a plan to add functionality for intra- and inter- synteny in the upcoming versions of RIdeogram? And is it possible to add gene coordinates adjacent to the chromosomes while plotting synteny?

[TickingClock1992]

Yes, of course. And, if you need to add intra- and inter- syntenic links now, you can send me your e-mail address. I will give you the raw script I used before for intra- and inter- synteny at chromosomal level and also gene synteny.

[evolgen]

Thanks a ton Hao - it is rohit@bioinf.uni-leipzig.de I might have missed something in the marker info, since it has chromosome number and coordinates with colors, but the species represented is absent. Is it possible to add a species column to a track label?