AlexsLemonade / AlexsLemonade/scpca-docs

Consider adding spatial data to the getting started section

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Python
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Description

This is a placeholder issue that it would probably be good to generally expand docs to include (a bit of!) getting started text on working with the spatial data. At this point we have enough knowledge to show this in R, but not yet Python.

It's worth noting as well - the way we currently disseminate spatial data cannot be straight-away* read into R with `SpatialExperiement::read10xVisium()` (although there are other frameworks to read in spatial data, this is the least clunky) since it doesn't like when _other files_ besides the `spatial` and the `*_feature_bc_matrix` folders are present at the same level. (I may try to file a PR to get that fixed, though...). Currently, you need to remove the html and json files, or place your spatial folder and desired matrix folder (raw or filtered) in its own folder. Note that it's fine if both raw and filtered are present though.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reviewing the getting started documentation and the existing spatial-data guidance. Document the R workflow, including the SpatialExperiement::read10xVisium() input limitation and the workaround of isolating the spatial and matrix folders; leave Python out until the project has enough knowledge to support it. Done means the R spatial-data setup and workaround are clearly explained.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, r
Domain
documentation
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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