Mark02 limit y axis rhat combined (#170)

src/pyggdrasil/visualize/_mcmc.py

@@ -223,13 +223,15 @@ def save_rhat_iteration_AD_DL(
     ax.set_xlabel("Iteration")  # type: ignore
     # get name of distance measure
     ax.set_ylabel(r"$\hat{R}$")  # type: ignore
+    ax.set_ylim(0.8, 5.0)  # type: ignore
     ax.plot(iteration, rhats_AD, color="darkgreen", label="AD")  # type: ignore
     ax.plot(iteration, rhats_DL, color="darkorange", label="DL")  # type: ignore
     # specifying horizontal line type
     # see limits https://arxiv.org/pdf/1903.08008.pdf
     plt.axhline(y=1.1, color="b", linestyle="--", linewidth=0.5)  # type: ignore
     plt.axhline(y=1.01, color="r", linestyle="-", linewidth=0.5)  # type: ignore
     ax.tick_params(axis="y", labelcolor="black")  # type: ignore
+    ax.set_yticks([1, 2, 3, 4, 5])  # type: ignore
     ax.legend(loc="upper right")  # type: ignore
     # ensure the output directory exists
     # strip the filename from the output path

workflows/visualize.smk

@@ -169,6 +169,7 @@ rule plot_rhat_AD_DL:
          plot="{DATADIR}/{experiment}/plots/{mcmc_config_id}/{mutation_data_id}/{base_tree_id}/AD_DL/rhat4-MCMCseeds_s{mcmc_seed1}_s{mcmc_seed2}_s{mcmc_seed3}_s{mcmc_seed4}-iTrees_i{init_tree_id1}_i{init_tree_id2}_i{init_tree_id3}_i{init_tree_id4}/rhat.svg",
     run:
          # load AD
+         change = 1 # nonsense change so that this rule is rerun 05/09/23
          in_fp = Path(input.rhat_AD)
          with open(in_fp) as f:
              data_AD = json.load(f)