Region view for sQTLs

[amkwong]

Our region view only shows eQTLs at the moment. To show sQTLs, we need to find a way to improve the performance of the API for sQTL data. Currently, requesting data for one specific transcript of a gene for a given study and tissue takes around half a minute.

The region data API accepts transcripts as an optional parameter, and that API is currently functional, though our region view page does not provide a way to visualize the results. With either the live server or locally with the provided test file, performance can be tested with a request for GTEx liver data, for one of the transcripts. Here is an example API call for SORT1 on the live server (this transcript and region can also be found in the test file):

https://fivex.sph.umich.edu/api/data/region/1/108774968-109774968/GTEx/liver/?gene_id=ENSG00000134243&datatype=txrev&transcript=ENST00000466471

Once the region view API of sQTLs has satisfactory performance, a few other minor changes will be necessary:

• The region page needs to be modified so that it can display sQTL data in addition to eQTL data. It may be necessary to modify the regional path to add eqtl/sqtl, similar to single-variant view.
• Linking to a region in single-variant sQTL view should bring you to a regional sQTL view, and vice versa (currently, clicking on a region in single-variant sQTL view brings you to the regional eQTL view)
• Add a button in region view that allows the user to toggle between eQTLs and sQTLs
  • This will require a smart way to recommend and request one transcript for each of the plot tracks so the plots aren't overwhelmed with data
• Add the option to choose from different transcripts in the pulldown menu, but highlight a "canonical" transcript for each gene (or use that transcript by default if no transcript is specified), so that the user will have some guidance on which of the many transcripts they may want to look at first