Merge pull request #32 from theislab/Zebrafish_readme_Bastiaanspanjaard

Updated and added description of downstream analysis scripts.

analysis/hu_zebrafish_linnaeus/README.rst

@@ -17,4 +17,5 @@ File description
     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. 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 <https://figshare.com/account/projects/163357/articles/22502974>`_.
+    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. 17). 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 <https://figshare.com/account/projects/163357/articles/22502974>`_.
+    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. 14-16.