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AlexsLemonade / scpca-docs

User information about ScPCA processing
https://scpca.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Add more SCE contents to merged objects page #237

Closed sjspielman closed 9 months ago

sjspielman commented 9 months ago

Towards #219

This PR adds more towards merged SCE file contents. I added the following sections:

The content mostly mirrors what's in sce_file_contents.md, but with some wording changes. Let me know what you think of phrasing throughout and if it all makes sense, and also whether we might want additional organization/subsections for the metadata.

sjspielman commented 9 months ago

I think this is now at a point where it's worth another look. I'm particularly interested in your thoughts on how I've presented the multiplex sample metadata here. Originally I was going to hold off on those until a future PR where I plan to add "additional considerations for multiplex" section, but given the different organization of the merged object compared to individual libraries, I think some of the way I've done it makes sense? Let me know if you agree or not!

I also found some things to fix along the way in sce_file_contents, including adding gene_ids as a rowData column, and updating a lot of the spots where we say "only present in filtered" -> "only present in filtered and processed".

sjspielman commented 9 months ago

Getting closer!!

sjspielman commented 9 months ago

I think I would move this sentence to be right after line 189 and state that just like merged objects with multiplexed libraries, all individual objects will contain the sample_metadata in the metadata slot.

@allyhawkins can you quickly peek at my wording for this in https://github.com/AlexsLemonade/scpca-docs/pull/237/commits/857c76f7e2e7ca2318aaf1bec185c75abadb3c82? Is this about what you had in mind?

allyhawkins commented 9 months ago

I think I would move this sentence to be right after line 189 and state that just like merged objects with multiplexed libraries, all individual objects will contain the sample_metadata in the metadata slot.

@allyhawkins can you quickly peek at my wording for this in 857c76f? Is this about what you had in mind?

Yea that looks good!