Improve thresholding 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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Improve thresholding plots #41

Closed lcolladotor closed 1 year ago

lcolladotor commented 2 years ago

Screen Shot 2022-05-18 at 1 21 38 PM

[x] Version control these plots (I couldn't find them, so maybe they are here on GitHub already). NVM! I see them at https://github.com/LieberInstitute/Visium_IF_AD/blob/master/plots/07_spot_qc/outliers/case_vs_control_pTau_scatter.pdf and https://github.com/LieberInstitute/Visium_IF_AD/blob/master/plots/07_spot_qc/outliers/case_vs_control_Abeta_scatter.pdf.
[x] Increase font size: you can use + theme_bw(base_size= 20) or 30 (try both out).
[x] If you can, you could use https://github.com/LieberInstitute/Visium_IF_AD/blob/0111d1d90d634ae4e2b21ebbbdbf3aaf84b76379/code/09_pathology_vs_BayesSpace/04_label_pathology_spots.R#L118 to check that the colors you chose are ok for those with visual impairements.
[x] Change y-axis label from percent to proportion
[x] Check with Sang Ho on whether we'll use AB (with greek letters) or Abeta. Louise could help you with this if needed.
[x] Update https://github.com/LieberInstitute/Visium_IF_AD/blob/master/plots/07_spot_qc/outliers/spe_whole_Abeta_scatter.pdf and https://github.com/LieberInstitute/Visium_IF_AD/blob/master/plots/07_spot_qc/outliers/spe_whole_pTau_scatter.pdf to match the same style as the other ones.