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Published 20 hours ago • verified publisher icon interactivereport

VIP Visualization in Plugin

Open xxlovexx1314 opened this issue 2 years ago • 8 comments

Hi Young, After I updated the VIPInterface.sh recently, I still meet the visualization problems, as the following picture: cf87707f2adb76724cc5ae78e4682f0 e: Any suggestions?

xxlovexx1314 avatar Oct 22 '21 03:10 xxlovexx1314

It might be caused by the page was opened without any interaction for too long. Does other plotting functions work?

You can also "git pull" the newest version, activate your env, and run "./update.VIPInterface.sh once". And let me know if this helps.

z5ouyang avatar Oct 30 '21 05:10 z5ouyang

I updated to the newest version, but it was not fixed. Does it matter with the JSPANEL? 5f47b1cb9d4fc4463fde2fb0eb47f51

xxlovexx1314 avatar Jan 14 '22 04:01 xxlovexx1314

@xxlovexx1314 sorry for the delay. Please "@" my name when you reply, so I can get notification. Do you still have issue? or did you try reinstall from fresh? thanks

z5ouyang avatar Apr 14 '22 05:04 z5ouyang

@z5ouyang I also get this error after building the VIP. I use the cellxgene gateway from Novartis and I noticed some errors in console: POST http://127.0.0.1:5005/view/pbmc3k.h5ad/VIP 500 (INTERNAL SERVER ERROR) and when I try to use the plugin, I get: Failed to load resource: the server responded with a status of 405 (METHOD NOT ALLOWED) I am using the latest code from cellxgene and VIP.

Any ideas what could go wrong?

eusebiu avatar Oct 05 '22 13:10 eusebiu

Also have this issue with the 405 error image

Dane-Z avatar Oct 11 '22 16:10 Dane-Z

Hi all, If this error shows on the initial loading, (rather than for each plot). The reason might be the version of "anndata" used to create h5ad files. Currently VIP uses anndata "0.7.4". We are working on updating the VIP to align with newer cellxgene version (removed a function we need) which uses newer anndata version.

z5ouyang avatar Oct 11 '22 16:10 z5ouyang

I was able to fix the 405 error using the solution from #35 (updating cellxgene-vip). However, I'm still running an older version of cellxgene to use cellxgene-vip because errors are thrown when launching certain datasets, or the VIP plugin doesn't showup, if using the newest version of cellxgene.

Very much looking forward to that update!

Dane-Z avatar Oct 11 '22 18:10 Dane-Z

Hi all, If this error shows on the initial loading, (rather than for each plot). The reason might be the version of "anndata" used to create h5ad files. Currently VIP uses anndata "0.7.4". We are working on updating the VIP to align with newer cellxgene version (removed a function we need) which uses newer anndata version.

@z5ouyang Any updates on when it will be available (the support for new cellxgene)? We are looking into starting a project and we would like to know which versions (of cellxgene and VIP) should we target.

eusebiu avatar Oct 12 '22 09:10 eusebiu

@eusebiu @Dane-Z If you run "config.sh" again in your conda env. will be using cellxgene v1.1.1

z5ouyang avatar Oct 28 '22 06:10 z5ouyang

Thanks a lot!

eusebiu avatar Oct 28 '22 08:10 eusebiu