PsychAD Scientific Data supplement

This relates to the publication: Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution

doi: TBA

Creating virtual environment

Using anaconda, and the env.yaml file provided here the following scripts can be run.

conda env create -f env.yml
conda activate psychad_scidata

psychad_plots.R

This script when run as:

Rscript psychad_plots.R

produces the following files:

Figures

• output_dir/plot_Fig2_dxDistr.pdf
• output_dir/plot_Fig2_dxDistr_ad_phenotypes_correlation.pdf
• output_dir/plot_Fig2_pie_age.pdf
• output_dir/plot_Fig2_pie_dxCat.pdf
• output_dir/plot_Fig2_pie_ethnicity.pdf
• output_dir/plot_Fig2_sexDistr.pdf
• output_dir/plot_Fig3_genoAncestryMerged.pdf
• output_dir/plot_Fig3_genoAncestrySnparray.pdf
• output_dir/plot_Fig3_genoSexCheck.pdf
• output_dir/plot_Fig5_dxAgeDist.pdf

Text

• output_dir/Table_2.csv
• output_dir/Table_S1.csv
• output_dir/Table_S3.csv

SciDatafigure_figs4.py

This script when run as:

python SciDatafigure_figs4.py

produces the following outputs:

• output_dir/Boxplot-fig4b-upper.pdf
• output_dir/Boxplot-fig4b-bottom.pdf
• output_dir/SciData_Fig4a.pdf
• output_dir/SciData_Fig4c.pdf
• output_dir/SciData_Fig4d.pdf