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LieberInstitute / Visium_SPG_AD

Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
https://research.libd.org/Visium_SPG_AD
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Create iSEE app for the pseudo-bulk data #52

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

Similar to https://github.com/LieberInstitute/spatialDLPFC/issues/80. Maybe Heena could help with this one? We'll figure it out.

lcolladotor commented 2 years ago

From /dcs04/lieber/lcolladotor/with10x_LIBD001/Visium_IF_AD/processed-data/11_grey_matter_only/wholegenome use sce_pseudo_pathology_wholegenome.rds. There's a similar file at /dcs04/lieber/lcolladotor/with10x_LIBD001/Visium_IF_AD/processed-data/11_grey_matter_only/targeted.

We might change these files, but well, that's where they'll live.

lcolladotor commented 2 years ago

Use the same pathology colors we use elsewhere. See sce_pseudo$path_groups_colors https://github.com/LieberInstitute/Visium_IF_AD/blob/cc26711a85fffa7363ced1883c2c8cb9a1f1701f/code/11_grey_matter_only/01_create_pseudobulk_data.R#L406

heenadivecha commented 2 years ago

The app for pseudobulk data (wholegenome) was created. The link to the app was shared to the members via slack