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kanaverse / kana

Single cell analysis in the browser
https://kanaverse.org/kana/
MIT License
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Possible to visualize pre-done clustering? #251

Closed ohmstead closed 9 months ago

ohmstead commented 9 months ago

Hi there,

kana looks like a beautiful tool for visualizing single-cell data. I'm wondering, is it possible to upload an .h5ad file that already has clusters annotated?

I've already performed my filtering, normalization, feature selection, dimension reduction, and clustering on my own. I would just like to explore my data interactively with kana.

If there is a better interaction/exploration tool out there, I would appreciate recommendations as well!

jkanche commented 9 months ago

@ohmstead, Kana does support an explore-mode, to explore pre-analyzed results. This wiki article should help you get started.

Let us know if you run into any issues.

ohmstead commented 9 months ago

@jkanche, I'm having trouble viewing my data in explore mode. I'm able to upload my AnnData .h5ad object, but I get the same error consistently: TypeError: Cannot convert undefined or null to object.

I don't know what "Feature type column name" means or what I'm supposed to select here. I only have RNA data in my adata object.

Here is the full log for a run:

10:10:19 AM: (downloadsdb) store initialized 10:10:19 AM: analysis state created 10:10:19 AM: bakana initialized 10:10:25 AM: preflight_input finished 10:11:26 AM: --- Analyis started--- 10:11:26 AM: TypeError: Cannot convert undefined or null to object

jkanche commented 9 months ago

@ohmstead, is it possible to share the h5ad object with us? or you can also point us to the file, If its a public dataset.

otherwise if you have h5dump installed, can you post the output on this file here?

ohmstead commented 9 months ago

@jkanche, I would be happy to. What is the best way privately share a link?

jkanche commented 9 months ago

lets see if we can debug this without sharing, can you post the output of h5dump?

ohmstead commented 9 months ago

I have h5dump installed on my Mac, but I'm not sure how to interface that with the webapp. It's not giving me an h5 log file to open, to my knowledge.

Can you walk me through?

jkanche commented 9 months ago

alright, can you share the file on google drive? (jayaram.kancherla@gmail.com)

jkanche commented 9 months ago

@ohmstead Thank you for sharing the file to identify the bug. In a few minutes the app (v3.0.20) will automatically update to the new version.

Thanks for reporting the issue and reach out if you run into more issues.

jkanche commented 9 months ago

Just tested on the deployed version and it works!

ohmstead commented 9 months ago

Yes it works for me as well! Thank you.