SpectraReproducibility
Notebooks for reproducing figures in the Spectra paper:
Supervised discovery of interpretable gene programs from single-cell data
https://doi.org/10.1101/2022.12.20.521311
Legend:
Figures:
| Figure | Notebook |
|---|---|
| Fig 1a | NA |
| Fig 1b | NA |
| Fig 1c | NA |
| Fig 1d | Kartha_PBMC_Spectra_expiMap.ipynb, Kartha_PBMC_plot_Slalom.ipynb |
| Fig 2a | NA |
| Fig 2b | Bassez_immune_figures.ipynb |
| Fig 2c | Bassez_Spectra_scHPF_NMF_Slalom_comparison.ipynb |
| Fig 2d | Bassez_immune_figures.ipynb |
| Fig 2e | Fig2E.ipynb ** |
| Fig 2f | Fig2F.ipynb ** |
| Fig 2g | Fig3D1.py, Fig3D2.py, benchmark-figures.py |
| Fig 3a | Bassez_immune_figures.ipynb |
| Fig 3b | Bassez_immune_figures.ipynb |
| Fig 3c | Bassez_immune_figures.ipynb |
| Fig 3d | Bassez_immune_figures.ipynb |
| Fig 3e | NA |
| Fig 3f | Bassez_immune_figures.ipynb |
| Fig 3g | NA |
| Fig 3h | Caushi_TIL_plotting.ipynb |
| Fig 4a | Bassez_immune_figures.ipynb |
| Fig 4b | Bassez_immune_figures.ipynb |
| Fig 4c | Bassez_immune_figures.ipynb |
| Fig 4d | Bassez_immune_figures.ipynb |
| Fig 5a | Bassez_immune_figures.ipynb |
| Fig 5b | Bassez_Milo.ipynb |
| Fig 5c | Bassez_invasion_factor.ipynb, Zhang_invasion_factor.ipynb |
| Fig 5d | Bassez_invasion_factor.ipynb, Zhang_invasion_factor.ipynb |
| Fig 6a | Salcher_TIL_plot.ipynb |
| Fig 6b | Salcher_TIL_plot.ipynb |
| Fig 6c | Salcher_TIL_plot.ipynb |
| Fig 6d | Salcher_TIL_plot.ipynb |
| Fig 6e | Salcher_TIL_plot.ipynb |
Supplementary Figures:
| Figure | Notebook |
|---|---|
| Fig S1a | Bassez_labeling_leukocytes.ipynb |
| Fig S1b | Zhang_labeling_leukocytes.ipynb |
| Fig S2a | Bassez_modelfiles.ipynb |
| Fig S2b | Bassez_modelfiles.ipynb |
| Fig S3a | Bassez_Spectra_scHPF_NMF_Slalom_comparison.ipynb, Bassez_expimap.ipynb |
| Fig S3b | Bassez_immune_figures.ipynb |
| Fig S3c | Bassez_immune_figures.ipynb |
| Fig S4a | Bassez_immune_figures.ipynb |
| Fig S4b | Bassez_immune_figures.ipynb |
| Fig S5a | Fig2E.ipynb |
| Fig S5b | ** |
| Fig S5c | ** |
| Fig S5d | FigS5D.ipynb |
| Fig S5e | FigS5E.ipynb |
| Fig S5f | FigS5F.ipynb |
| Fig S5g | Fig3D1.py, Fig3D2.py, benchmark-figures.py |
| Fig S5h | benchmark-figures.py |
| Fig S6a | ** |
| Fig S6b | Bassez_immune_figures.ipynb |
| Fig S6c | Bassez_immune_figures.ipynb |
| Fig S6d | Bassez_immune_figures.ipynb |
| Fig S6e | Bassez_Spectra_scHPF_NMF_Slalom_comparison.ipynb, Bassez_expimap.ipynb |
| Fig S6f | Bassez_immune_figures.ipynb, Bassez_expimap.ipynb, Bassez_Spectra_scHPF_NMF_Slalom_comparison |
| Fig S6g | Bassez_immune_figures.ipynb, Bassez_expimap.ipynb, Bassez_Spectra_scHPF_NMF_Slalom_comparison |
| Fig S7a | ** |
| Fig S7b | Bassez_immune_figures.ipynb |
| Fig S7c | Bassez_immune_figures.ipynb, Bassez_Spectra_scHPF_NMF_Slalom_comparison, Bassez_expimap.ipynb |
| Fig S7d | Bassez_immune_figures.ipynb, Bassez_Spectra_scHPF_NMF_Slalom_comparison, Bassez_expimap.ipynb |
| Fig S7e | Bassez_immune_figures.ipynb, Bassez_Spectra_scHPF_NMF_Slalom_comparison, Bassez_expimap.ipynb |
| Fig S8a | Bassez_immune_figures.ipynb |
| Fig S8b | Bassez_immune_figures.ipynb |
| Fig S8c | Bassez_immune_figures.ipynb |
| Fig S8d | Bassez_immune_figures.ipynb |
| Fig S8e | Bassez_modelfiles.ipynb |
| Fig S8f | Bassez_invasion_factor.ipynb |
| Fig S8g | ** |