Recapitulating a GenomeBrowser-style plot

Question

[LChart]

I'm trying to visualize some cut&tag data, and would like to re-capitulate a plot that looks like this:

The key features I'm looking for are:

1. The ability to vertically highlight regions [though I'm OK doing this in post, too]
2. The presence of tracks without "boxes" around them -- including the gene track on the bottom
3. The ability to show individual reads as "dots" or "dashes" (the "snow" effect)

The font for the track heights seem to suggest that this is IGV, but I haven't been able to customize it to do this (remove track boundaries, show reads as tiny dashes as opposed to the standard IGV read display). I'm open to some equivalent way of obtaining this display (in, say, WashU epigenome browser or UCSC genome browser).

Thanks

Answer 1

[cmdcolin]

Millefy is somewhat similar https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6542-z

Signac also https://stuartlab.org/signac/articles/visualization

My list of "single cell tagged tools" for genomic data visualization https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Single%20cell

I agree it looks like igv but i don't know how to make igv conjure up such a display

[LChart]

Millefy looks great! It's close enough to what I want that I'm accepting it as the answer. Thanks!

Answer 2

[bk11]

Have your tried PyGenomeTracks? It is a cool package to visualize any genetic data.

https://pygenometracks.readthedocs.io/en/latest/content/examples.html

[LChart]

New to me. I don't see anything in the examples covering (3) -- do you know of a way to do this?

[bk11]

I believe it should be doable.