Lollipop plots for structural variation coordinates

Question

[Dimitri]

Hi!

I'm a research intern with a (relatively) amateur skill level at industry-standard bioinformatics techniques. Currently, I have a bunch of files (mostly .bed's and derivatives of .vcf's) containing specific coordinates for the locations of structural variations in a specific chromosome.

I'm trying to generate a series of lollipop plots to see and visualize whether these variations all cluster around a certain area to get a better grasp about this type of variation and the specific gene it's associated with. I've attempted the trackViewer modules with little luck, as I'm not the most well-versed with R, and the documentation doesn't seem to work for my file types. Is there any way for me to either modify these files to correspond to simple .bed files with coordinates, or is there an easier approach to do this?

Thanks in advance for your help, and I look forward to your replies! Much appreciated :)

Answer 1

[Shred]

The lollipop chart you've posted is better suited for SNP visualization. You could try instead Samplot for visualization of structural variants. https://github.com/ryanlayer/samplot

Answer 2

[Trivas]

I feel like a manhattan plot would be useful here, maybe start with https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html