AlexsLemonade / AlexsLemonade/scpcaTools

Support spatial data in coldata_to_df()

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R
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Description

In , @allyhawkins created a function `spatial_coldata_to_df()` that adds some of the data from the `spatialData` slot of a SpatialExperiment to the main `colData` contents after merging.

For scpcaTools, I think it would make sense to wrap that functionality into `coldata_to_df()`, where the function would check whether we were working with a SpatialExperiment, and if so, merge all contents of the `spatialData` slot with the `colData` contents.

There is a small wrinkle in that we expect `spatialData` to go away in a future version of the `SpatialExperiment` package https://github.com/drighelli/SpatialExperiment/issues/84. We should plan to deal with that case as we write this for futureproofing.

Contributor guide

Open the contributing guide

Research direction

Start by reading coldata_to_df() and the existing spatial_coldata_to_df() function mentioned in the issue to understand how colData and spatialData are merged. Check how SpatialExperiment identifies these data slots and account for the planned removal of spatialData; done means coldata_to_df() handles SpatialExperiment inputs while preserving existing behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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