Scripts used to reproduce all figures in "Identification of perturbation-responsive regions and genes in comparative spatial transcriptomics atlases".
R/figures/ # one script per figure panel (see table below)
R/functions/ # shared utility functions
R/theme.R # shared ggplot theme
All scripts are in R/figures/. Each calls setwd('~/git/vespucci-analysis/') at the top and reads data via the data/ symlink. Output PDFs are written to fig/ inside this repo.
| Figure | Script |
|---|---|
| Fig 1 | main-fig1.R |
| Fig 2 | main-fig2.R |
| Fig 3 | main-fig3.R |
| Fig 4 | main-fig4.R |
| Fig 5 | main-fig5.R |
| Figure | Script(s) |
|---|---|
| EFig 1 | supp-simulations-example-genes.R |
| EFig 2 | supp-simulations-performance.R |
| EFig 3 | supp-simulations-additional-metrics.R |
| EFig 4 | supp-simulations-false-discoveries.R |
| EFig 5 | supp-simulations-resolutions-size.R |
| EFig 6 | supp-simulations-tests.R + supp-real-data-tests.R |
| EFig 7 | supp-koupourtidou.R |
| EFig 8 | supp-calcagno.R |
| EFig 9 | supp-maniatis.R |
| EFig 10 | supp-kathe.R |
| EFig 11 | supp-zeng.R |
| EFig 12 | — |
| EFig 13 | supp-regen.R |
| EFig 14 | supp-spatial-cluster-genes.R |
| EFig 15 | supp-registration-effect.R |
| EFig 16 | supp-feature-importance.R |