Update deconvolution plots - Githubissues

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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Update deconvolution plots #83

Closed lcolladotor closed 1 year ago

lcolladotor commented 1 year ago

Hi Nick,

From our meeting with Sang Ho and Kristen today, we have a few requests for the spot deconvolution plots.

[x] Subset to only the AD samples in the gray matter spots https://github.com/LieberInstitute/Visium_SPG_AD/tree/master/plots/21_spot_deconvo/explore_results. That is, use https://github.com/LieberInstitute/Visium_SPG_AD/blob/69108f24d99790af74876ca58952592e0026761a/code/22_gene_pairs_path/01_gene_pairs_path.R#L30-L31.
[x] For https://github.com/LieberInstitute/Visium_SPG_AD/blob/master/plots/21_spot_deconvo/explore_results/pathology_barplots_inverted.pdf and https://github.com/LieberInstitute/Visium_SPG_AD/blob/master/plots/21_spot_deconvo/explore_results/pathology_boxplots.pdf use the pathology colors we have. You can re-use https://github.com/LieberInstitute/Visium_SPG_AD/blob/69108f24d99790af74876ca58952592e0026761a/code/22_gene_pairs_path/01_gene_pairs_path.R#L205-L209 + scale_fill_manual() like at https://github.com/LieberInstitute/Visium_SPG_AD/blob/69108f24d99790af74876ca58952592e0026761a/code/22_gene_pairs_path/01_gene_pairs_path.R#L177.
[x] If you can remake all 3 plots for all spots (and/or just the white matter ones), those extra plots could be useful for just internal purposes. This item is of lower priority though.

Thanks, Leo