search

IGS / gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
https://umgear.org
GNU Affero General Public License v3.0
14 stars 4 forks source link

Incorperate SWNE into gEAR sc workbench #409

Open JPReceveur opened 2 years ago

JPReceveur commented 2 years ago

Had a user ask about whether SWNE plots are going to be supported in gEAR. Allowing for static plots with SWNE labels is covered in #382, based on an ask from another user, but should SWNE be an option in the single cell workbench? It seems to be gaining in popularity.

adkinsrs commented 2 years ago

We would have to run a custom tool to perform these analyses, as scanpy does not currently have functionality for these types of plots. I did a quick check of the scanpy github issues page, and there are no issues with "SWNE", so I believe there has not been any interest to incorporate it into scanpy either.

adkinsrs commented 2 years ago

Another hurdle is that SWNE seems to only be implemented in R, so we would have to run rpy2 to get it to work with our API/CGI calls

jorvis commented 2 years ago

Given our priorities on other tasks right now, I'd say to create a ticket requesting support within scanpy and then address it at a future date as our priorities allow. This could possibly even include adding it to scanpy via a PR ourselves.

adkinsrs commented 2 years ago

https://github.com/scverse/scanpy/issues/2308

JPReceveur commented 2 years ago

Just adding a +1 here for another user group who wants this functionality