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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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Question - Linking cellBrowser through another web-app with dynamic data selection #246

Closed tkakar closed 1 year ago

tkakar commented 2 years ago

I'm building a web-app (vue + node) where I want to link cellBrowser (hosted on a local S3 bucket) for our own data selected dynamically and was wondering if anyone else has done it? My understanding is to add the data in the output directory and update the configuration file. Or having all the data in the output directory and only select the needed one (dynamically selected via the app) in the configuration file. Would love to hear any suggestions or other ways to achieving this. Thanks.

maximilianh commented 2 years ago

Sorry I don’t understand. What do you mean with “link cellBrowser” and “our own data selected dynamically” ?

On Wed 1 Jun 2022 at 19:54, Tabassum Kakar @.***> wrote:

I'm building a web-app (vue + node) where I want to link cellBrowser (hosted on a local S3 bucket) for our own data selected dynamically and was wondering if anyone else has done it? My understanding is to add the data in the output directory and update the configuration file. Or having all the data in the output directory and only select the needed one (dynamically selected via the app) in the configuration file. Would love to hear any suggestions or other ways to achieving this. Thanks.

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tkakar commented 2 years ago

by dynamically selecting data, I meant a particular patient that a user on the web-app is interested in and want to explore their single cell data. The gene expression, tsne coordinates etc are provided for each patient.

maximilianh commented 2 years ago

Can’t you build one cell browser dataset per patient and then just link to the right dataset with the ds=xxx parameter ?

On Wed 1 Jun 2022 at 23:14, Tabassum Kakar @.***> wrote:

by dynamically selecting data, I meant a particular patient that a user on the web-app is interested in and want to explore their single cell data. The gene expression, tsne coordinates etc are provided for each patient.

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tkakar commented 2 years ago

That seems much easier. Thanks for the suggestion. I'll try that.

maximilianh commented 2 years ago

The cell browser has built-in support for many datasets, all of them are shown as a list if you don't provide the ds=parameter. You can look at cells.ucsc.edu what this looks like.

As long as you run cbBuild with the same html output directory, any new dataset added with cbBuild will simply add to the this long list of datasets.

But of course you can always add the ?ds= to the URL and that will open a particular dataset.

e.g. cells.ucsc.edu/?ds=cortex-dev.

This is the reason every dataset needs to have a name.

I hope this helps. Let us know if you have other questions.

On Thu, Jun 2, 2022 at 3:04 PM Tabassum Kakar @.***> wrote:

That seems much easier. Thanks for the suggestion. I'll try that.

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matthewspeir commented 2 years ago

Hi, @tkakar, if all is good with Max's '?ds=' suggestion, can we close this ticket?

tkakar commented 2 years ago

Hi sorry I haven’t gotten a chance to implement it yet. I’ll try next week.

Thanks.

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From: Matt Speir @.> Sent: Monday, June 13, 2022 6:22:24 PM To: maximilianh/cellBrowser @.> Cc: Kakar, Tabassum @.>; Mention @.> Subject: [EXT] Re: [maximilianh/cellBrowser] Question - Linking cellBrowser through another web-app with dynamic data selection (Issue #246)

Hi, @tkakarhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftkakar&data=05%7C01%7Ctkakar%40wpi.edu%7Cecb642dcff4c4201733b08da4d8b316d%7C589c76f5ca1541f9884b55ec15a0672a%7C0%7C0%7C637907557469137867%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BdPXXLUshKJj8FzH4MAIWP7rwnFUBfEQT%2Fk2osWzfCc%3D&reserved=0, if all is good with Max's '?ds=' suggestion, can we close this ticket?

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maximilianh commented 1 year ago

Does this mean that you implemented something?

On Thu, Sep 15, 2022 at 8:43 PM Tabassum Kakar @.***> wrote:

Closed #246 https://github.com/maximilianh/cellBrowser/issues/246 as completed.

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tkakar commented 1 year ago

Hi Max,

Focus got shifted towards other priorities at the moment.

Tabassum

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From: Maximilian Haeussler @.> Sent: Thursday, September 15, 2022 4:51:37 PM To: maximilianh/cellBrowser @.> Cc: Kakar, Tabassum @.>; State change @.> Subject: [EXT] Re: [maximilianh/cellBrowser] Question - Linking cellBrowser through another web-app with dynamic data selection (Issue #246)

Does this mean that you implemented something?

On Thu, Sep 15, 2022 at 8:43 PM Tabassum Kakar @.***> wrote:

Closed #246 https://github.com/maximilianh/cellBrowser/issues/246 as completed.

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