add prc and auroc to metrics plots

Author: aryarm

analysis/workflow/scripts/midway_manhattan_summary.py

@@ -303,7 +303,7 @@ def main(
 
     # if this is a pval, take the -log10 of it
     if not bic:
-        tsfm_pval = lambda pval: -np.log10(pval)
+        tsfm_pval = lambda pval: -np.log10(pval) if pval != 0 else np.inf
     else:
         tsfm_pval = lambda val: val
 
@@ -422,7 +422,7 @@ def main(
     log.debug(f"Found {vals.shape[0]} points")
 
     # remove any vals that were NA (but got converted to 0)
-    # and also any vals that were greater than max-val
+    # and also any vals that were greater than max-val (which defaults to inf)
     na_rows = (vals == 0).any(axis=1) | (vals >= max_val).any(axis=1)
     not_na_rows_idxs = {k: v[~na_rows] for k,v in axes_idxs.items()}
     if color is not None:
@@ -551,10 +551,11 @@ def main(
     ax.set_xlabel(case_type + ": " + ax_labs[1])
     ax.set_ylabel(case_type + ": " + ax_labs[0])
     ax.axline((0,0), (max_val, max_val), linestyle="--", color="orange")
-    ax.axline((0,thresh), (thresh, thresh), color="red")
-    ax_histx.axline((thresh,0), (thresh, thresh), color="red")
-    ax.axline((thresh,0), (thresh, thresh), color="red")
-    ax_histy.axline((0,thresh), (thresh, thresh), color="red")
+    if thresh != 0:
+        ax.axline((0,thresh), (thresh, thresh), color="red")
+        ax_histx.axline((thresh,0), (thresh, thresh), color="red")
+        ax.axline((thresh,0), (thresh, thresh), color="red")
+        ax_histy.axline((0,thresh), (thresh, thresh), color="red")
     ax_histy.spines['top'].set_visible(False)
     ax_histx.spines['top'].set_visible(False)
     ax_histy.spines['right'].set_visible(False)

analysis/workflow/scripts/midway_summary_metrics.py

@@ -111,8 +111,8 @@ def main(
 
     log.info("Creating plots")
     fig, axs = plt.subplots(
-        nrows=1, ncols=3,
-        sharex=True, figsize=(7, 3),
+        nrows=1, ncols=5,
+        sharex=True, figsize=((7/3)*5, 3),
         constrained_layout=True, tight_layout=False,
     )
 
@@ -123,14 +123,31 @@ def main(
         metrics_beta = metrics[params["beta"] == beta]
 
         axs[0].plot(params_beta["sampsize"], metrics_beta["FPR"], "o", label=beta)
+        axs[0].set_ylim((-0.001, 0.051))
         axs[0].set_ylabel("False positive rate")
 
         axs[1].plot(params_beta["sampsize"], metrics_beta["Recall"], "o")
+        axs[1].set_ylim((-0.001, 1.001))
         axs[1].set_ylabel("Recall")
 
         axs[2].plot(params_beta["sampsize"], metrics_beta["Significance Threshold"], "o")
+        max_alpha = max(metrics_beta["Significance Threshold"])
+        if max_alpha > 1:
+            axs[2].set_ylim((-2.001, 10.001))
+        elif max_alpha < 0.25:
+            axs[2].set_ylim((-0.001, 0.251))
+        else:
+            axs[2].set_ylim((-0.001, 1.001))
         axs[2].set_ylabel("Significance threshold")
 
+        axs[3].plot(params_beta["sampsize"], metrics_beta["AUROC"], "o")
+        axs[3].set_ylim((0.495, 1.001))
+        axs[3].set_ylabel("AUROC")
+
+        axs[4].plot(params_beta["sampsize"], metrics_beta["Average Precision"], "o")
+        axs[4].set_ylim((0.495, 1.001))
+        axs[4].set_ylabel("Average Precision")
+
     log.info("Writing figure")
     fig.supxlabel("Sample size")
     fig.legend(loc="lower right", ncol=len(betas), fontsize="small")