The analysis of the zebrafish data is a two-step process:
- Calculation of transition matrices using moslin.
- Downstream analysis of the transition matrices.
The input data files can be found on figshare: adata file with the scRNA-seq data under Zebrafish heart regeneration and the lineage data as a .pkl file at Zebrafish reconstructed trees.
| File | What it does |
|---|---|
| run_hu_moslin.sh (run_hu_lot.sh) | Helper script used by run_sbatch_hu_moslin.py (run_sbatch_hu_lot.py ). Calls the relevant functions from utils.py to run the simulations and performance analysis using moslin (LineageOT) mapping. |
| run_sbatch_hu_moslin.py (run_sbatch_hu_lot.py) | Main SLURM script to calculate the couplings between the hearts at consecutive time points. Calling the command python3 run_sbatch_hu_moslin.py will instantiate sbatch calls to calculate all couplings using moslin (LineageOT). The output of each coupling is saved as a .csv file under data/hu_zabrafish_linnaeus/output/. |
| hu_moslin_fit_couplings.py (hu_lot_fit_couplings.py) | Main function called by run_hu_moslin.sh (run_hu_lot.sh). fit_couplings_all() is used to compute the couplings between all hearts at consecutive time points for the given input moslin arguments, alpha, epsilon, beta, and tau_a (given LineageOT argument epsilon). The couplings are saved as .csv files under DATA_DIR/output/. |
| Zebrafish_coupling_analysis.R | Downstream analysis script to generate alluvial plots as shown in Figs. 4f and 4g, as well as visualization of the transition matrices (Figs. 4b and 4c, Supp. Fig. 20). Apart from the couplings generated in the previous step, the downstream analysis additionally uses data files for single-cell annotation, cell type colors, lineage information and sample timepoints found here. |
| Hyperparameters_with_persistency.py | Downstream analysis script to determine optimal hyperparameter values using the cell type persistency test and validating the optimal hyperparameters on transient fibroblasts. Used to generate Figs. 4d and 4e, as well as Supp. Figs. 17-19. |