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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
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change labeling in layout #187

Closed LisaSikkema closed 2 years ago

LisaSikkema commented 4 years ago

Hi,

First of all thanks for building this tool, it's really awesome and helpful.

I was wondering if there's a way for changing the labels that are shown in the layout. It seems like by default, it only shows the labels from the category provided under --clusterField. Is it possible to show the labels for any annotation of choice? That would be really useful!

Best, Lisa

matthewspeir commented 4 years ago

Hello, Lisa.

Thank you for your question! You can change the labels shown in the layout by changing the "labelField" option in your cellbrowser.conf: https://github.com/maximilianh/cellBrowser/blob/48675f82f54652fd34abfb68427550aafa4428be/src/cbPyLib/cellbrowser/sampleConfig/cellbrowser.conf#L66.

maximilianh commented 4 years ago

Hi Lisa, thanks for the nice words. how did you create your cell browser? From the command line? From R?

LisaSikkema commented 4 years ago

Hi! Thanks for the quick reply. I created it from the command line. I'm guessing the change in the conf file would require me to relaunch cellbrowser every time I want to change the labeling? I was hoping for an option to do this using a button within cellbrowser, instead of having to relaunch.

matthewspeir commented 4 years ago

Yes, there is no way to control the field used for labels from the cell browser UI at this time. The field has to be selected through the cellbrowser.conf before starting the cell browser.

This is a great feature suggestion though, and one we've heard from a few others. We're keen to implement it, but I don't have an estimate of when we will have a chance to do so.

devashishmohanta commented 2 years ago

Hi @matthewspeir

This is a query regarding the "labelField" Change in the cellbrowser.conf file. Since it has to be changed every time before cbBuild operations, Is there any other way where we can dynamically change the labels in the layout according to the Annotation. Similar to what "Color By Annotation" function does, can there be "labels by Annotation" feature activated by incorporating any changes in the code. It will be really helpful if you can suggest any method to resolve the issue.

Thanks Debashish

matthewspeir commented 2 years ago

Hi @devashishmohanta,

This feature is currently 'in development', though we're planning to release it soon. @maximilianh has a few more bugs to resolve with it.

You can preview it via the develop branch of the github repo (or maybe even via pip install --pre cellbrowser?) if you don't want to wait for the full pip release.

maximilianh commented 2 years ago

Or also on cells-test.gi.UCSC.edu

On Tue 12 Apr 2022 at 17:18, Matt Speir @.***> wrote:

Hi @devashishmohanta https://github.com/devashishmohanta,

This feature is currently 'in development', though we're planning to release it soon. @maximilianh https://github.com/maximilianh has a few more bugs to resolve with it.

You can preview it via the develop branch of the github repo (or maybe even via pip install --pre cellbrowser?) if you don't want to wait for the full pip release.

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/187#issuecomment-1096864461, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TNHWO7MUVMMA5SEOATVEWH3DANCNFSM4QQRIYZQ . You are receiving this because you were mentioned.Message ID: @.***>

devashishmohanta commented 2 years ago

Thank you @maximilianh and @matthewspeir it was a great help.

maximilianh commented 2 years ago

Hi, do you like the feature as we have it now? Any feedback on it? We plan to release it soon and can still add improvements or wishes now...

On Mon, Apr 18, 2022 at 11:00 AM DEBASHISH MOHANTA @.***> wrote:

Thank you @maximilianh https://github.com/maximilianh and @matthewspeir https://github.com/matthewspeir it was a great help.

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/187#issuecomment-1101237458, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TOFGXTVLQGGV6QWOMDVFUQCFANCNFSM4QQRIYZQ . You are receiving this because you were mentioned.Message ID: @.***>

matthewspeir commented 2 years ago

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

Feel free to open a new ticket to report any bugs or improvements!