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statgen / localzoom

Make interactive LocusZoom plots from a local GWAS file
https://statgen.github.io/localzoom/
MIT License
7 stars 4 forks source link

How to change the LDserver setting #19

Closed psytky03 closed 2 years ago

psytky03 commented 2 years ago

Hi! I would like to use an in-house LDserver, how could I change the settings?

abought commented 2 years ago

Greetings! Apologies for not seeing this question sooner.

I wasn't aware that anyone was forking this particular repo! But strictly speaking, you could change this URL, assuming that you are running an instance of Michigan LDServer software that exposes a particular API.

(Since this is a standalone app that makes certain assumptions about our LD server, certain other things are hardcoded and might take more spelunking to change- most notably the list of LD populations in the "choose LD population" dropdown) https://github.com/statgen/localzoom/blob/fbe95d129e6a70c184e2a08da403cea5d582980d/src/util/constants.js#L2

If you want to customize the plot, without all the extra point-and-click UI contrls of LocalZoom, the core plotting widget is LocusZoom.js, which offers detailed docs and examples for talking to your own data provider or tabix files.

abought commented 2 years ago

An alternative would be to add your own LD from plink-output LD calculations, using a tabix file. (there are instructions in the UI). It's a much more restrictive workflow, so if you're comfortable running your own UM LD server, that is definitely a more powerful approach.

I'll close this ticket for now but feel free to follow up with any further questions.