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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
105 stars 42 forks source link

Allow a change to the cluster field #69

Closed maximilianh closed 2 years ago

maximilianh commented 5 years ago

Needed for @slowkow as they have a dataset merge.

Probably needed for ciona.

Could be tucked away under View > Cluster Field, shows a dropdown and just does a call.

Otherwise right-click is still there, on fields.

PriyankaOyx commented 2 years ago

Hi @maximilianh

Thanks a lot for this amazing tool. I was wondering if there is a way to add pop-up markers for multiple cluster assignments?

For instance, I have clustered the 10x data using both louvain and leiden algorithm (for testing purposes) and have a column assigned to celltypes. I wanted to have an option to click and check markers based on label annotation (which i think is currently applicable to only clusterField). I tried making changes to the config file to provide multiple clusterFields but that just created more problems.

Any solution for the same? Any guidance would be highly appreciated.

maximilianh commented 2 years ago

Yes! Have a look at cells-test.gi.ucsc.edu. It's on the left side menu, just select a different "Cluster Field" @mxposed added the code a while ago. Let us know if you have any feedback on it. It's not released yet, but coming very soon to the public site, I need to remove numeric fields from it and make sure that after a change of the layout the label fields are redrawn. Thanks for the feedback!

PriyankaOyx commented 2 years ago

Thanks a ton, that's a great help. Hope to see the update in the development version too.

But for now the issue is resolved.

matthewspeir commented 2 years ago

I think we can close this now that the 'label by annotation' feature is available.