Update app.py

app.py

@@ -7,7 +7,10 @@ import igraph as ig
 
 # print(os.pwd())
 
-species_to_imgpath = {'bird': './descendent_specific_topk_heatmap_withbb_ep=last_024+051'}
+species_to_imgpath = {'bird': './descendent_specific_topk_heatmap_withbb_ep=last_024+051',
+                      'fish': './descendent_specific_topk_heatmap_withbb_ep=last_024+051',
+                      'butterfly': './descendent_specific_topk_heatmap_withbb_ep=last_024+051',
+                     }
 
 # this has to be there for each species
 imgname_to_filepath = {} # this ignores the extension such as .png
@@ -184,10 +187,111 @@ def plot_tree_using_igraph():
 
     return fig
 
+def plot_tree_from_species(species_name):
+    # Define the edges in a tree structure
+    # edges = [(0, 1), (0, 2), (1, 3), (1, 4), (2, 5), (2, 6)]
+
+    imgpath = species_to_imgpath[species_name]
+    print(imgpath)
+    root = get_tree(imgpath)
+
+    # root = ROOT
+    edges = create_binary_tree_edges(root)
+    # edges = [(str(n1), str(n2)) for (n1, n2) in edges]
+
+    # print(edges)
+    
+    # Create an igraph Graph from the edge list
+    g = ig.Graph(edges, directed=True)
+    
+    # Validate the root index
+    if g.vcount() > 0:  # Check if the graph has any vertices
+        root_vertex_id = 0  # This assumes that vertex '0' is the root
+    else:
+        print("The graph has no vertices.")
+        return None
+
+    # Use the Reingold-Tilford layout to position the nodes
+    try:
+        layout = g.layout_reingold_tilford(root=None)  # Correct root specification
+    except Exception as e:
+        print(f"Error computing layout: {e}")
+        return None
+
+    # Edge traces
+    edge_x = []
+    edge_y = []
+    for edge in edges:
+        start_idx, end_idx = edge
+        x0, y0 = layout.coords[start_idx]
+        x1, y1 = layout.coords[end_idx]
+        edge_x.extend([x0, x1, None])
+        edge_y.extend([-y0, -y1, None])  # y values are inverted to make the tree top-down
+
+    edge_trace = go.Scatter(
+        x=edge_x, y=edge_y,
+        line=dict(width=0.5, color='#888'),
+        hoverinfo='none',
+        mode='lines')
+
+    # Node traces
+    node_x = [pos[0] for pos in layout.coords]
+    node_y = [-pos[1] for pos in layout.coords]  # y values are inverted
+
+    node_trace = go.Scatter(
+        x=node_x, y=node_y,
+        text=[id_to_node[i].name for i in range(len(layout.coords))],
+        # text=["Node {}".format(i) for i in range(len(layout.coords))],
+        mode='markers+text',
+        hoverinfo='text',
+        marker=dict(
+            showscale=False,
+            size=10,
+            color='LightSkyBlue'
+        ),
+        textposition="bottom center"
+    )
+
+    # Create a Plotly figure
+    fig = go.Figure(data=[edge_trace, node_trace],
+                    layout=go.Layout(
+                        title='<b>Tree Layout with iGraph and Plotly</b>',
+                        titlefont_size=16,
+                        showlegend=False,
+                        hovermode='closest',
+                        margin=dict(b=0, l=0, r=0, t=50),
+                        xaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
+                        yaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
+                        # height=600,
+                        # width=600,
+                        annotations=[dict(
+                            showarrow=False,
+                            xref="paper", yref="paper",
+                            x=0.005, y=-0.002 )]
+                    ))
+
+    return gr.Plot(fig)
+
+def set_nodename_to_protoIDs(species_name):
+    global nodename_to_protoIDs
+    imgpath = species_to_imgpath[species_name]
+    for foldername in os.listdir(imgpath):
+        if os.path.isdir(os.path.join(imgpath, foldername)):
+            folderpath = os.path.join(imgpath, foldername)
+            for filename in os.listdir(folderpath):
+                if filename.endswith('png') or filename.endswith('jpg'):
+                    filepath = os.path.join(folderpath, filename)
+                    imgname_to_filepath[filename] = filepath
+                    nodename = filename.split('.')[0].split('-')[0]
+                    protoID = filename.split('.')[0].split('-')[1]
+                    nodename_to_protoIDs[nodename].append(protoID)
+
 
 def get_protoIDs(nodename):
     return gr.Dropdown(choices=nodename_to_protoIDs[nodename], interactive=True)
 
+def get_nodenames(species_name):
+    return gr.Dropdown(choices=list(nodename_to_protoIDs.keys()), interactive=True)
 
 def get_image(nodename, protoID):
     imgname = '-'.join([nodename, protoID]) + '.png'
@@ -202,26 +306,72 @@ with gr.Blocks() as demo:
     ROOT = get_tree(imgpath)
     print(ROOT.name)
     gr.Markdown("## Interactive Tree and Image Display")
-    # with gr.Row():
-    #     dropdown_species = gr.Dropdown(label="Select a species", choices=list(species_to_imgpath.keys()))
         
-    with gr.Row():
-        tree_output = gr.Plot(plot_tree_using_igraph)  # Connect the function directly
+    # with gr.Row():
+    #     tree_output = gr.Plot(plot_tree_using_igraph)  # Connect the function directly
     
+    # with gr.Row():
+    #     with gr.Column():
+    #         dropdown_1_nodename = gr.Dropdown(label="Select a node name", choices=list(nodename_to_protoIDs.keys()))
+    #         dropdown_1_protos = gr.Dropdown(label="Select a prototype ID", choices=[], allow_custom_value=True)
+    #         image_output_1 = gr.Image()
+    #     with gr.Column():
+    #         dropdown_2_nodename = gr.Dropdown(label="Select a node name", choices=list(nodename_to_protoIDs.keys()))
+    #         dropdown_2_protos = gr.Dropdown(label="Select a prototype ID", choices=[], allow_custom_value=True)
+    #         image_output_2 = gr.Image()
+
+    # dropdown_1_nodename.change(get_protoIDs, dropdown_1_nodename, dropdown_1_protos)
+    # dropdown_1_protos.change(get_image, [dropdown_1_nodename, dropdown_1_protos], image_output_1)
+    # dropdown_2_nodename.change(get_protoIDs, dropdown_2_nodename, dropdown_2_protos)
+    # dropdown_2_protos.change(get_image, [dropdown_2_nodename, dropdown_2_protos], image_output_2)
+
+    with gr.Row():
+        dropdown_species = gr.Dropdown(label="Select a species", choices=list(species_to_imgpath.keys()))
+    with gr.Row():
+        tree_output = gr.Plot()  # Connect the function directly
     with gr.Row():
         with gr.Column():
-            dropdown_1_nodename = gr.Dropdown(label="Select a node name", choices=list(nodename_to_protoIDs.keys()))
+            dropdown_1_nodename = gr.Dropdown(label="Select a node name", choices=[])
             dropdown_1_protos = gr.Dropdown(label="Select a prototype ID", choices=[], allow_custom_value=True)
             image_output_1 = gr.Image()
         with gr.Column():
-            dropdown_2_nodename = gr.Dropdown(label="Select a node name", choices=list(nodename_to_protoIDs.keys()))
+            dropdown_2_nodename = gr.Dropdown(label="Select a node name", choices=[])
             dropdown_2_protos = gr.Dropdown(label="Select a prototype ID", choices=[], allow_custom_value=True)
             image_output_2 = gr.Image()
-
+    dropdown_species.change(plot_tree_from_species, dropdown_species, tree_output)
+    dropdown_species.change(set_nodename_to_protoIDs)
+    dropdown_species.change(get_nodenames, dropdown_species, dropdown_1_nodename)
+    dropdown_species.change(get_nodenames, dropdown_species, dropdown_2_nodename)
     dropdown_1_nodename.change(get_protoIDs, dropdown_1_nodename, dropdown_1_protos)
     dropdown_1_protos.change(get_image, [dropdown_1_nodename, dropdown_1_protos], image_output_1)
     dropdown_2_nodename.change(get_protoIDs, dropdown_2_nodename, dropdown_2_protos)
     dropdown_2_protos.change(get_image, [dropdown_2_nodename, dropdown_2_protos], image_output_2)
+
+    # imgpath = species_to_imgpath['bird']
+    # print(imgpath)
+    # ROOT = get_tree(imgpath)
+    # print(ROOT.name)
+    # gr.Markdown("## Interactive Tree and Image Display")
+        
+    # with gr.Row():
+    #     tree_output = gr.Plot(plot_tree_using_igraph)  # Connect the function directly
+    
+    # with gr.Row():
+    #     with gr.Column():
+    #         dropdown_3_nodename = gr.Dropdown(label="Select a node name", choices=list(nodename_to_protoIDs.keys()))
+    #         dropdown_3_protos = gr.Dropdown(label="Select a prototype ID", choices=[], allow_custom_value=True)
+    #         image_output_3 = gr.Image()
+    #     with gr.Column():
+    #         dropdown_4_nodename = gr.Dropdown(label="Select a node name", choices=list(nodename_to_protoIDs.keys()))
+    #         dropdown_4_protos = gr.Dropdown(label="Select a prototype ID", choices=[], allow_custom_value=True)
+    #         image_output_4 = gr.Image()
+
+    # dropdown_3_nodename.change(get_protoIDs, dropdown_3_nodename, dropdown_3_protos)
+    # dropdown_3_protos.change(get_image, [dropdown_3_nodename, dropdown_3_protos], image_output_3)
+    # dropdown_4_nodename.change(get_protoIDs, dropdown_4_nodename, dropdown_4_protos)
+    # dropdown_4_protos.change(get_image, [dropdown_4_nodename, dropdown_4_protos], image_output_4)
+
+    
         
 
 # Initialize with placeholder images