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AlexsLemonade / scpcaTools

BSD 3-Clause "New" or "Revised" License
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Support spatial data in coldata_to_df() #77

Open jashapiro opened 2 years ago

jashapiro commented 2 years ago

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.

jaclyn-taroni commented 2 years ago

I am going to slot this for next sprint for discussion. From what's written, it does seem like this could be an enhancement that we don't need to do.

allyhawkins commented 2 years ago

I would say that this is no longer needed, since we aren't doing any import of the spatial output into spatial experiments in R at all currently. It might be helpful to have in the package if we ever were planning to do downstream analysis on spatial libraries, but this isn't necessary for processing the spatial data to be available on the portal.

jaclyn-taroni commented 2 years ago

I'm going to remove this from the sprint and the Epic.