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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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Update PCA plots for the region analysis #120

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

The PCA plots (currently not version controlled) from https://github.com/LieberInstitute/spatialDLPFC/tree/main/plots/09_region_differential_expression don't match the style from those at https://github.com/LieberInstitute/spatialDLPFC/tree/main/plots/08_layer_differential_expression, so I know that they are older plots.

Some things these don't have are:

Screen Shot 2022-07-15 at 12 25 47 PM

Compare against https://github.com/LieberInstitute/spatialDLPFC/blob/main/plots/08_layer_differential_expression/pca_explanatory_variables_k2.pdf.

By the way, note that at 08_layer_differential_expression the color legend includes colors not used. It's a small detail that we don't need to deal with right now, but well, just take in into account when updating 09_region_differential_expression.

This makes me think that some other parts of the DE analysis at the region level are incomplete or not up to date. I know this was by design since we wanted to figure out the code well with the layer DE analysis before doing the region DE one. So we might need to chat about filterByExpr() + the statistical model used for the region analysis.

abspangler13 commented 2 years ago

thanks @lcolladotor. as you noted the region analysis is not finished yet. The model is not correct and there are probably some other issues still. That's why the plots haven't been polished yet.