Possible to visualize pre-done clustering?

[ohmstead]

Possible to visualize pre-done clustering?

[ohmstead]

Yes it works for me as well! Thank you.

[jkanche]

@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]

@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]

@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]

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

[jkanche]

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

[ohmstead]

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]

alright, can you share the file on google drive? ([email protected])

[jkanche]

@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]

Just tested on the deployed version and it works!