fix plot

app.py

@@ -490,35 +490,65 @@ if selected_model == 'Cas9':
                 st.experimental_rerun()
 
 elif selected_model == 'Cas12':
-    def visualize_and_generate_files(df, gene_sequence, exons, gene_symbol):
+    def visualize_genomic_data():
         fig = go.Figure()
-        # Exon visualization
-        for exon in exons:
-            exon_start, exon_end = exon['start'], exon['end']
-            fig.add_trace(go.Bar(
-                x=[(exon_start + exon_end) / 2],
-                y=[0.5], width=[exon_end - exon_start],
-                base=0, marker_color='purple',
-                name='Exon'
-            ))
-
-        # Prediction visualization
-        for index, row in df.iterrows():  # Iterate over DataFrame rows safely
-            midpoint = (row['Start Pos'] + row['End Pos']) / 2  # Ensure columns are correctly referenced
-            fig.add_trace(go.Scatter(
-                x=[midpoint],
-                y=[1],
-                mode='markers',
-                marker=dict(size=10, color='blue'),
-                name=f'Prediction {index + 1}'
-            ))
 
+        EXON_BASE = 0  # Base position for exons and CDS on the Y axis
+        EXON_HEIGHT = 0.02  # How 'tall' the exon markers should appear
+
+        # Plot Exons as small markers on the X-axis
+        for exon in st.session_state['exons']:
+            try:
+                exon_start, exon_end = int(exon['start']), int(exon['end'])
+                fig.add_trace(go.Bar(
+                    x=[(exon_start + exon_end) / 2],
+                    y=[EXON_HEIGHT],
+                    width=[exon_end - exon_start],
+                    base=EXON_BASE,
+                    marker_color='rgba(128, 0, 128, 0.5)',
+                    name='Exon'
+                ))
+            except ValueError:
+                st.error("Error in exon positions. Exon positions should be numeric.")
+
+        VERTICAL_GAP = 0.2  # Gap between different ranks
+
+        # Define max and min Y values based on strand and rank
+        MAX_STRAND_Y = 0.1  # Maximum Y value for positive strand results
+        MIN_STRAND_Y = -0.1  # Minimum Y value for negative strand results
+
+        # Iterate over top 5 sorted predictions to create the plot
+        for i, prediction in enumerate(st.session_state['on_target_results'][:5], start=1):  # Only top 5
+            try:
+                start, end = int(prediction['Start Pos']), int(prediction['End Pos'])
+                midpoint = (start + end) / 2
+                strand = prediction['Strand']
+                y_value = (MAX_STRAND_Y - (i - 1) * VERTICAL_GAP) if strand in ['1', '+'] else (
+                            MIN_STRAND_Y + (i - 1) * VERTICAL_GAP)
+
+                fig.add_trace(go.Scatter(
+                    x=[midpoint],
+                    y=[y_value],
+                    mode='markers+text',
+                    marker=dict(symbol='triangle-up' if strand in ['1', '+'] else 'triangle-down', size=12),
+                    text=f"Rank: {i}",
+                    hoverinfo='text',
+                    hovertext=f"Rank: {i}<br>Chromosome: {prediction['Chr']}<br>Target Sequence: {prediction['Target']}<br>gRNA: {prediction['gRNA']}<br>Start: {start}<br>End: {end}<br>Strand: {'+' if strand in ['1', '+'] else '-'}<br>Transcript: {prediction['Transcript']}<br>Prediction: {prediction['Prediction']:.4f}",
+                ))
+            except ValueError:
+                st.error("Error in prediction positions. Start and end positions should be numeric.")
+
+        # Update layout for clarity and interaction
         fig.update_layout(
-            title='Cas12 Prediction Visualization',
-            xaxis_title='Position',
-            yaxis=dict(tickvals=[0.5, 1], ticktext=['Exons', 'Predictions']),
-            showlegend=True
+            title='Top 5 gRNA Sequences by Prediction Score',
+            xaxis_title='Genomic Position',
+            yaxis_title='Strand',
+            yaxis=dict(tickvals=[MAX_STRAND_Y, MIN_STRAND_Y], ticktext=['+', '-']),
+            showlegend=False,
+            hovermode='x unified',
         )
+
+        # Display the plot
         st.plotly_chart(fig)
 
         # File generation and download