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igvteam / spacewalk

Spacewalk is an application for displaying and interacting with super-resolution chromatin tracing data in 3D. SpaceWalk includes igv.js and juicebox.js instances for rapid and intuitive visual comparison and interaction between 3D data and 1D genomic data.
MIT License
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Walking along the IGV tracks doesn't work in the shared links #262

Closed gnir closed 1 year ago

gnir commented 1 year ago

Hello @turner and @jrobinso,

I've noticed that if I load a track bed file from a URL, I can move my mouse along that track and the corresponding area will show on the spacewalk trace. But, when I share this view with my collaborators, they can't do so with the link I shared with them Here is an example Guy

jrobinso commented 1 year ago

@turner Also, clicking on the track selection boxes in IGV does not affect the color of the spacewalk structure view. It looks like the IGV track and SW are decoupled.

turner commented 1 year ago

I'll take a look.

turner commented 1 year ago

@gnir @jrobinso here is a shareable url of a possible fix: https://tinyurl.com/2esuqntc

Still very laggy due to the high number of renderable objects (~1.5M). Jim the igv panel menus should work better. I am now using a branch of igvjs and discarded the local hacked copy I had been using.

The test app is here: https://deploy-preview-263--spacewalk-site.netlify.app/

gnir commented 1 year ago

Hi @turner,

I am still unable to walk along the bed track and see the corresponding region in the trace. Thank you, Guy

turner commented 1 year ago

@gnir hmmm. Try this and let me know if you can "walk" in the igvjs panel: https://tinyurl.com/2dut374c

This is a smaller point cloud file. I want to try and isolate the issue.

gnir commented 1 year ago

@turner - no, I can't. Guy

turner commented 1 year ago

@gnir, what if you launch the test app https://deploy-preview-263--spacewalk-site.netlify.app/ (rather then using a share url) and open the file. Do you see the same result as when you use the share url I provided?

turner commented 1 year ago

@gnir I think I have an idea about what's happing. I'm working on a fix now.

gnir commented 1 year ago

@turner, great! I can tell you that when I loaded the files from URL it worked for me. But when I shared with others, it didn't work for them. Guy

turner commented 1 year ago

@gnir ok I think it got it. Try this share url: https://tinyurl.com/2ov6lzcz

gnir commented 1 year ago

@turner - working, thank you!

turner commented 1 year ago

Great. Go ahead and use the production app now. https://spacewalk-site.netlify.app/

This test app - and the shareable url based on it - will go away in a or two.

turner commented 1 year ago

@gnir I've reopened this issue with news of a significant speed up.

Check it out and let me know what you think: https://tinyurl.com/2nhsrg2h

This update is now live in the production app: https://spacewalk-site.netlify.app/

gnir commented 1 year ago

Tested and it's soooooo much faster! Guy