diff --git a/src/pyggdrasil/visualize/_mcmc.py b/src/pyggdrasil/visualize/_mcmc.py index 013ad981..2faa4e0a 100644 --- a/src/pyggdrasil/visualize/_mcmc.py +++ b/src/pyggdrasil/visualize/_mcmc.py @@ -223,6 +223,7 @@ 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 @@ -230,6 +231,7 @@ def save_rhat_iteration_AD_DL( 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 diff --git a/workflows/visualize.smk b/workflows/visualize.smk index a59483b9..6a44fd8b 100644 --- a/workflows/visualize.smk +++ b/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)