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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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When generating a browser (or manually afterwards), be able to choose which meta field to color cells on in the default view #2

Closed e-t-k closed 6 years ago

e-t-k commented 6 years ago

Right now, when a new user loads the browser, the cells are colored by "Seurat Cluster".

I would like to be able to configure the browser when it is being set up such that I can choose a different default field to color the cells.

For example, I would like to be able to configure the browser so that the cells are colored by "disease" when when a new user loads the browser.

This could be via a parameter to the cpPrep, or by manually editing a file (config.json ? index.html?) after creation, or whatever makes sense.

maximilianh commented 6 years ago

To my surprise, cbPrep already has an option for that:

-l CLUSTERLABEL, --clusterLabel=CLUSTERLABEL default field with the cluster label, from the meta data table.

e-t-k commented 6 years ago

Thanks! We'll try this out the next time we generate a dataset.

maximilianh commented 6 years ago

you can just rerun the command, it wont do the full run again, just update the options.

you can also change it in your html file.

On Thu, Oct 12, 2017 at 12:38 PM, e-t-k notifications@github.com wrote:

Hi Max, Thanks! We'll try this out the next time we generate a dataset.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/2#issuecomment-336243727, or mute the thread https://github.com/notifications/unsubscribe-auth/AAS-TY0jbuTAvj4bkuywe_5yuM-UjO_Aks5srmq8gaJpZM4P3gXs .

maximilianh commented 6 years ago

I've added documentation how to change the dataset config.