Visualizing human genomic loci

Question

[James]

Hi everyone, I want to be able to generate a genomic loci figure that looks like below, where I can mark loci of interest over the entire genome (I got the figure from this paper: https://www.nature.com/articles/s41598-022-15058-0)

Would you have any recommendation on where / how I could prepare the figure like this? I have some experience using UCSC genome browser, but the output I get from it is not as neat as this figure. Thank you.

edit: I have checked out Artemis, ggbio, genVisR, genoverse, and a couple other tools I found from this forum, but none of them seemed like exactly what I needed. Thanks again!

[Yogi]

Did you double check that they don't discuss the software used in the "Methods section"?

[James]

Hi Yogi, Yes, I have read the methods section and there was no particular mentioning of the software that was used to create the figure. I think I have some good leads now. Thanks!

Answer 1

[Michael]

There are a lot of tools to plot chromosome ideograms with data and there are a lot of posts here:

• Drawing Chromosome Ideograms With Data
• Ideogram.js: a JavaScript library for chromosome visualization
• Drawing yeast chromosome ideograms with data

(Some of the links found above might not work anymore)

RIdeogram: https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html

Gviz: https://www.bioconductor.org/packages/devel/bioc/html/Gviz.html

karyotypeR: https://bernatgel.github.io/karyoploter_tutorial/

[James]

Hi Michael, thank you very much for your comment with lots of great information!