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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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Adding multiple count matrix files in the label counts in the config file for the cbBuild #241

Open devashishmohanta opened 2 years ago

devashishmohanta commented 2 years ago

Hello, cell browser developers,

I had a query regarding the count matrix input. Does the cell browser allow using multiple count matrix data in the cellbrowser.conf file to use it for cbBuild operation so that multiple counts matrix data can be used. This is similar to what I am looking for: image

It will really helpful if you can any way to it

Thanks and Regards Debashish

matthewspeir commented 2 years ago

Hi, @devashishmohanta .

Sorry for the delay. Currently, we can only display the expression values from one expression matrix.

This is something @maximilianh is interested in implementing. It would allow someone to flip between raw counts, normalized expression, etc. Although I don't know what the time line is for that work.

maximilianh commented 1 year ago

Hi, thanks for this feedback.

You can supply multiple matrices like this:

matrices=[ {'label':'counts','fileName':'counts_exprMatrix.tsv.gz'}, {'label':'data','fileName':'data_exprMatrix.tsv.gz'}, {'label':'scale','fileName':'scale_exprMatrix.tsv.gz'}]

But this will be used for downloads only. Right now these are not used for coloring it. I assume you want

On Mon, Apr 18, 2022 at 1:07 PM DEBASHISH MOHANTA @.***> wrote:

Hello, cell browser developers,

I had a query regarding the count matrix input. Does the cell browser allow using multiple count matrix data in the cellbrowser.conf file to use it for cbBuild operation so that multiple counts matrix data can be used. This is similar to what I am looking for: [image: image] https://user-images.githubusercontent.com/43270576/163799780-5a01660d-bdd9-4d9d-8114-6c4d43ab733b.png

It will really helpful if you can any way to it

Thanks and Regards Debashish

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/241, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TKS734AV7TW4XFON63VFU65ZANCNFSM5TVTFGMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

maximilianh commented 1 year ago

Hi @devashishmohanta are you still interested in this feature?

On Fri, May 27, 2022 at 12:55 AM Matt Speir @.***> wrote:

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

Sorry for the delay. Currently, we can only display the expression values from one expression matrix.

This is something @maximilianh https://github.com/maximilianh is interested in implementing. It would allow someone to flip between raw counts, normalized expression, etc. Although I don't know what the time line is for that work.

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/241#issuecomment-1139126027, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TJR42SBF4C2SEVY7RLVL76N5ANCNFSM5TVTFGMA . You are receiving this because you were mentioned.Message ID: @.***>