Replicate clinical enrichment results

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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Replicate clinical enrichment results #111

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

We want to replicate the results from Figure 6 from the Nat Neuro paper. That will involve adapting this script Andrew wrote: https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/check_clinical_gene_sets.R. I think that we had some supplementary figures that were also related to this, and if so, we'll want to replicate them too.

If @kmartinow @kmaynard12 have other gene sets that they would like to check, we'll add them to the list. But first, let's replicate the results from before.

Thanks!

lcolladotor commented 2 years ago

This is related to https://github.com/LieberInstitute/spatialDLPFC/issues/79, although #79 is about choosing what example data to show on the shiny apps as well as making spatialLIBD more flexible so users (like you in this case) can choose what data is shown on the app.

abspangler13 commented 2 years ago

[x] @lcolladotor still waiting to finish this with the two gene sets that I can't load. We can talk about it in my meeting on Tuesday. See https://github.com/LieberInstitute/spatialLIBD/issues/39
[x] redo plots now that I fixed problem with two datasets
[x] polish plots, fix plotting errors