Mouse_CSC_PNAS

Figure-generation code for:

Singh, Jin, Hu, Palazzo, Cano, Hoang, Bhutto, Wang, Sinha, Blackshaw, Qian, and Handa. Molecular underpinnings of induced degenerative heterogeneity in the retinal pigment epithelium. PNAS, 2026.

This repository organizes the analysis code used to generate Figures 1-3 of the paper. The scripts were refactored from the working analysis file All_figures_v12.R into one script per published figure.

Repository Layout

• code/00_setup.R - shared package loading, paths, annotation tables, and plotting helpers.
• code/01_figure1_snRNA_seq.R - Figure 1: snRNA-seq RPE/dedifferentiated RPE panels.
• code/02_figure2_snATAC_seq.R - Figure 2: snATAC-seq/accessibility panels.
• code/03_figure3_transcriptional_phenotype.R - Figure 3: DEG, KEGG, EMT/senescence/mitochondrial panels.
• code/run_all_figures.R - runs the three figure scripts in order.
• data/README.md - expected input files and where to place them.
• CODE_REVIEW.md - notes from refactoring and issues fixed from the original script.

Quick Start

Run from the repository root:

source("code/run_all_figures.R")

or run one figure at a time:

Rscript code/01_figure1_snRNA_seq.R
Rscript code/02_figure2_snATAC_seq.R
Rscript code/03_figure3_transcriptional_phenotype.R

By default, scripts look for inputs under data/ and write outputs under figures/. You can keep large data outside git and point the scripts to it:

export MOUSE_CSC_DATA_DIR="/path/to/Mouse_CSC_PNAS_data"
export MOUSE_CSC_FIGURE_DIR="/path/to/output_figures"
Rscript code/run_all_figures.R

Notes

The repository intentionally excludes large .RData, .rds, fragment, and generated figure files. See data/README.md for the expected local data layout.