fix

app.py

@@ -190,32 +190,32 @@ if selected_model == 'Cas9':
                 # Initialize Plotly figure
                 fig = go.Figure()
 
-                # Adjust these constants for appearance
-                LINE_WIDTH = 2  # Width of EXON and CDS lines
-                EXON_OPACITY = 0.5  # Make exon lines semi-transparent
+                EXON_HEIGHT = 0.03  # How 'tall' the exon markers should appear
+                CDS_HEIGHT = 0.05  # How 'tall' the CDS markers should appear
+                Y_POS = -0.1  # Position on the Y axis to place these markers
 
-                # Ensure EXON and CDS are drawn at the same Y position on the X-axis
-                EXON_CDS_Y_POS = 0  # Directly on the X-axis
-
-                # Draw EXONs
+                # Plot Exons as small markers on the X-axis
                 for exon in st.session_state['exons']:
                     exon_start, exon_end = exon['start'], exon['end']
-                    fig.add_trace(go.Scatter(
-                        x=[exon_start, exon_end],
-                        y=[EXON_CDS_Y_POS, EXON_CDS_Y_POS],
-                        mode='lines',
-                        line=dict(color='purple', width=LINE_WIDTH, opacity=EXON_OPACITY),
+                    # Using bars for better control over width and position
+                    fig.add_trace(go.Bar(
+                        x=[(exon_start + exon_end) / 2],  # Position at the center of the exon
+                        y=[EXON_HEIGHT],
+                        width=[exon_end - exon_start],  # Width of the bar is the exon length
+                        base=[Y_POS],
+                        marker_color='rgba(128, 0, 128, 0.5)',  # Purple color with transparency
                         name='Exon'
                     ))
 
-                # Draw CDSs
+                # Plot CDS in a similar manner
                 for cds in st.session_state['cds']:
                     cds_start, cds_end = cds['start'], cds['end']
-                    fig.add_trace(go.Scatter(
-                        x=[cds_start, cds_end],
-                        y=[EXON_CDS_Y_POS, EXON_CDS_Y_POS],
-                        mode='lines',
-                        line=dict(color='blue', width=LINE_WIDTH + 1),  # Slightly thicker than EXON
+                    fig.add_trace(go.Bar(
+                        x=[(cds_start + cds_end) / 2],  # Position at the center of the CDS
+                        y=[CDS_HEIGHT],
+                        width=[cds_end - cds_start],  # Width of the bar is the CDS length
+                        base=[Y_POS - EXON_HEIGHT],  # Slightly offset from the exons
+                        marker_color='rgba(0, 0, 255, 1)',  # Blue color, more solid
                         name='CDS'
                     ))