AMP-PD_SciData

This relates to the publication: A multi-region single nucleus transcriptomic atlas of Parkinson’s disease

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

pd-metadata-overview.R

This script when run as:

Rscript pd-metadata-overview.R

produces the following output files:

• output_dir/plot_age_by_diagnosis.pdf
• output_dir/plot_pd_phenotypes_correlation_spearman.pdf
• output_dir/plot_age_by_sex.pdf
• output_dir/plot_race.pdf
• output_dir/plot_avgCellCountPerDiss_byBrainRegion.pdf
• output_dir/plot_sampleCount_byBrainRegion.pdf
• output_dir/plot_braak_by_brainbank.pdf
• output_dir/plot_sampleCount_byBrainRegion_Upset.pdf
• output_dir/plot_brainbank.pdf
• output_dir/plot_sex_by_brainbank.pdf
• output_dir/plot_cellCount2.pdf
• output_dir/plot_sex.pdf
• output_dir/plot_diagnosis_by_brainbank.pdf
• output_dir/plot_totalCellCount_byBrainRegion.pdf
• output_dir/plot_diagnosis.pdf
• output_dir/plot_fig_4a_coverageDistrPlot.pdf
• output_dir/plot_fig_4b_coverageBoxPlot.pdf
• output_dir/plot_fig_4c_snpsPlot.pdf
• output_dir/plot_fig_4d_indelsPlot.pdf
• output_dir/plot_geno_ancestry_merged.pdf

This script is designed to run as is when the whole git repo is downloaded. Otherwise please fix line 10 to reflect your working directory.

qtltools_plot_dash_SciData.py

This script when run as:

python qtltools_plot_dash_SciData.py

produces the following outputs:

• output_dir/SciData_fig4h.pdf

SciDatafigure_figs3abc.py

This script when run as:

python SciDatafigure_figs3abc.py

produces the following outputs:

• output_dir/SciData_fig3a.pdf
• output_dir/SciData_fig3b_1.pdf
• output_dir/SciData_fig3b_2.pdf
• output_dir/SciData_fig3c.pdf