2114INF

This repository contains processed, analysis-ready tables and R scripts to reproduce the figures in the 2114INF paper.

Repository structure

• data/tables/: base analysis-ready tables (metadata, CyTOF frequencies, Olink NPX, …)
• scripts/figures/: figure scripts (one script per panel)
• scripts/lib/: shared helpers (loading tables, common functions)
• scripts/export/: scripts that rebuild data/tables/ from the current workspace sources
• output/: locally generated figures

Re-generate base tables

From repository root:

Rscript scripts/export/export_base_tables.R

Reproduce figures

Examples:

Rscript scripts/figures/fig2/Fig2A_growth_zscores.R
Rscript scripts/figures/fig5/Fig5B_mds_panelB_timepoint.R
Rscript scripts/figures/fig6/Fig6D_cytof_topClusters_PCA_timepoint.R

By default, scripts write PDFs into output/figures/manuscript/.