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LieberInstitute / spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
http://research.libd.org/spatialDLPFC/
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Prepare external data to show for spatial registration and clinical enrichment #79

Closed lcolladotor closed 1 year ago

lcolladotor commented 2 years ago

spatialLIBD itself will need to be updated for this. But well, in the meantime, we'll need to prepare the data that the app uses for the layer-level panel. We'll like to show the psychENCODE or other data that we'll process as part of the paper instead of the current example data shown.

Screen Shot 2022-05-07 at 12 16 35 PM Screen Shot 2022-05-07 at 12 16 29 PM

spatialLIBD will need to be improved so you can pass multiple tables with some names and potentially descriptions (those could be part of the documentation at the layer-level data panel). I'm thinking that it'll be 2 extra arguments to spatialLIBD::run_app() that will take named list() objects.

Some of the scripts at https://github.com/LieberInstitute/spatialLIBD/tree/master/data-raw that prepared the example data that currently spatialLIBD uses will be useful.

This will have to wait until we have the other datasets we want to show. But you can start with the Tran et al, Neuron, 2021 data subsetted to DLPFC. Ask Nick, Louise or Matt for help with this if needed.

I think that it'll be best if you plan to save these Rdata files at https://github.com/LieberInstitute/spatialDLPFC/tree/main/code/deploy_app since we'll have to deploy them from there (unlike the default processed-data path).

lcolladotor commented 1 year ago

Not really needed for now. Closing for now, though we could come back to this.