improve html report

yztxwd · yztxwd · commit 8cbaf78f9858 · 2026-02-26T19:38:26.000-05:00
diff --git a/tpcav/cavs.py b/tpcav/cavs.py
@@ -25,7 +25,7 @@
 from sklearn.linear_model import LinearRegression
 import logomaker
 
-from . import helper, utils
+from . import helper, utils, report
 from .concepts import ConceptBuilder
 from .tpcav_model import TPCAV
 from matplotlib import gridspec
@@ -615,7 +615,7 @@ def load_custom_motif_info(key):
             cavs_fscores_df['AUC_fscores_residual'] = residuals
             plot_reg(data=cavs_fscores_df, x='avg_len', y='AUC_fscores', ax=axes[0])
             plot_reg(data=cavs_fscores_df, x='avg_gc', y='AUC_fscores', ax=axes[1])
-            axes[2].set_axis('off')
+            axes[2].axis('off')
 
         cavs_fscores_df.sort_values("AUC_fscores_residual", ascending=False, inplace=True)
     else:
@@ -648,7 +648,9 @@ def run_tpcav(
     num_pc: Union[str,int]='full',
     p=1, 
     max_pending_jobs=4,
-    save_cav_trainer=True
+    save_cav_trainer=True,
+    generate_html_report=True,
+    html_report_fscore_thresh=0.9,
 ):
     """
     One-stop function to compute CAVs on motif concepts and bed concepts, compute AUC of motif concept f-scores after correction
@@ -765,4 +767,9 @@ def run_tpcav(
     else:
         cavs_fscores_df = None
 
+    if generate_html_report:
+        report.generate_tcav_html_report(str(output_path / f"report.html"), motif_cav_trainers,
+                                         extra_cav_trainers = {'bed concepts': bed_cav_trainer},
+                                         motif_file=motif_file, motif_file_fmt=motif_file_fmt, fscore_thresh=html_report_fscore_thresh)
+
     return cavs_fscores_df, motif_cav_trainers, bed_cav_trainer
diff --git a/tpcav/report.py b/tpcav/report.py
@@ -100,7 +100,7 @@ def generate_tpcav_html_report(
     fscore_thresh: float = 0.8,
     top_motif_concepts: int = 10,
     title: str = "TPCAV report",
-    embed_images: bool = True,
+    embed_images: bool = False,
 ) -> Path:
     """
     Generate a standalone HTML report from CavTrainer objects.
@@ -435,6 +435,14 @@ def _to_list(x: Any) -> Any:
             f"<div class='muted'>Images are stored in: {_html.escape(str(assets_dir))}</div>"
         )
 
+    param_rows = [
+        ("fscore_thresh", str(fscore_thresh)),
+        ("top_motif_concepts", str(top_motif_concepts)),
+        ("motif_file", str(motif_file) if motif_file is not None else ""),
+        ("motif_file_fmt", str(motif_file_fmt)),
+    ]
+    params_html = _render_kv_table(param_rows)
+
     all_concepts: list[str] = []
     seen = set()
     for c in ranked_motif_concepts:
@@ -739,12 +747,13 @@ def _png_html(path: Path, alt: str) -> str:
   </style>
 </head>
 <body>
-	  <div class="container">
-	    <header>
-	      <h1>{_html.escape(title)}</h1>
-	      <div class="meta">Generated: {now}</div>
-	      {assets_note}
-	    </header>
+		  <div class="container">
+		    <header>
+		      <h1>{_html.escape(title)}</h1>
+		      <div class="meta">Generated: {now}</div>
+		      {params_html}
+		      {assets_note}
+		    </header>
 
 			    <section>
 			      <h2>Concepts</h2>
