search

tanaylab / mcATAC

Metacell analysis for ATAC data
https://tanaylab.github.io/mcATAC/
Other
1 stars 0 forks source link

plot_tracks_at_locus issue #43

Closed RoniSto closed 2 years ago

RoniSto commented 2 years ago

In plot_tracks_at_locus, if you choose to plot an interval and not a gene TSS extended left and right, you lose the option to plot gene expression. There should be an option to plot a specified interval (like a TAD) and still show gene expression on the side.

yonatans2 commented 2 years ago
  1. This is a feature request, not an issue (issue = suspected bug).
  2. This feature does exist, you have the parameter rna_vals in which you can supply gene expression values.
  3. In order to make "automatic" gene expression plotting for an arbitrary interval, we'll need to make a lot of use-/edge-case decisions, like: what if there are a lot of genes in that interval, how do you choose automatically which one to plot? what if you specify a gene and the gene is not in the interval at all (could be by mistake or on purpose), should the function check this and then abort or warn? I'm happy to discuss this, and execute if this is a common use case, but it seems like a considerable amount of work for something that can be done pretty easily without all these checks.