Add descriptions for plotly buttons (an embeded HTML)

Author: Ahren09

config/BMCBioinformatics2021.json

@@ -5,7 +5,7 @@
   "interpolation": 0.2,
   "idx_reference_snapshot": 30,
   "num_nearest_neighbors": [20],
-  "projected_nodes": [1022, 6285, 4683, 6777, 7345, 3148, 10220, 6753, 4601, 3481, 51444, 9517, 51205, 9360, 1068, 9229, 1017, 1981, 9218, 55024],
+  "projected_nodes": [1022, 6285, 4683, 6777, 7345, 3148, 10220, 6753, 4601, 3481, 51444, 9517, 51205, 9360, 1068, 9229, 1017, 1981, 9218, 55024, 306, 1520, 2212, 1281, 1277, 1287],
   "perplexity": 20,
   "reference_nodes": "reference_nodes.json"
 }

config/HistWords-CN-GNN.json

@@ -0,0 +1,10 @@
+{
+  "embedding_dim": 128,
+  "idx_reference_snapshot": 4,
+  "interpolation": 0.2,
+  "model_name": "GConvGRU",
+  "num_nearest_neighbors": [20],
+  "perplexity": 20,
+  "projected_nodes": ["节约", "资源", "生态", "环境", "绿色", "气候", "地球"],
+  "reference_nodes": "reference_nodes.json"
+}

dygetiviz/__init__.py renamed to dygetviz/__init__.py

@@ -127,6 +127,8 @@ def load_data() -> dict:
 
     elif args.dataset_name == "BMCBioinformatics2021":
 
+        plot_anomaly_labels = True
+
         metadata_df = pd.read_excel(
             osp.join("data", args.dataset_name, "metadata.xlsx"))
         metadata_df = metadata_df.rename(columns={"entrez": "node"})

dygetiviz/arguments.py renamed to dygetviz/arguments.py

@@ -0,0 +1,71 @@
+# Import libraries
+import dash
+from dash import dcc, html
+from dash.dependencies import Input, Output
+import plotly.express as px
+import pandas as pd
+
+# Sample data
+df = pd.DataFrame({
+    'x': [1, 2, 3, 4, 5],
+    'y': [1, 4, 2, 3, 5],
+    'name': ['A', 'B', 'C', 'D', 'E']
+})
+
+# Create a Dash app
+app = dash.Dash(__name__)
+
+# Define the app layout
+app.layout = html.Div([
+    dcc.Graph(
+        id='scatter-plot',
+        config={'staticPlot': False, 'displayModeBar': True},
+        figure=px.scatter(df, x='x', y='y')
+    )
+])
+
+# List to keep track of current annotations
+annotations = []
+
+
+# Callback to annotate point on click
+@app.callback(
+    Output('scatter-plot', 'figure'),
+    Input('scatter-plot', 'clickData')
+)
+def display_click_data(clickData):
+    global annotations
+    if clickData:
+        point_data = clickData['points'][0]
+        idx = point_data['pointIndex']
+        point_name = df['name'].iloc[idx]
+
+        # Check if the point is already annotated
+        existing_annotation = next((a for a in annotations if
+                                    a['x'] == point_data['x'] and a['y'] ==
+                                    point_data['y']), None)
+
+        if existing_annotation:
+            # Remove existing annotation
+            annotations.remove(existing_annotation)
+        else:
+            # Add new annotation
+            annotations.append({
+                'x': point_data['x'],
+                'y': point_data['y'],
+                'xref': 'x',
+                'yref': 'y',
+                'text': point_name,
+                'showarrow': False
+            })
+
+    fig2 = go.Figure()
+
+    fig = px.scatter(df, x='x', y='y')
+    fig.update_layout(annotations=annotations)
+    return fig
+
+
+# Run the app
+if __name__ == '__main__':
+    app.run_server(debug=False, port=8049)

dygetiviz/const.py renamed to dygetviz/const.py

@@ -0,0 +1,24 @@
+from Bio import Entrez
+
+
+def get_gene_name_by_entrez_id(entrez_id):
+    Entrez.email = "[email protected]"  # Always tell NCBI who you are
+    handle = Entrez.efetch(db="gene", id=entrez_id, retmode="xml")
+    records = Entrez.read(handle)
+
+    # The gene name can usually be found in the "Gene-ref" field, under "locus"
+    try:
+        gene_name = records[0]["Entrezgene_gene"]["Gene-ref"]["Gene-ref_locus"]
+        return gene_name
+    except (KeyError, IndexError):
+        return None
+
+
+entrez_id = 5296
+gene_name = get_gene_name_by_entrez_id(entrez_id)
+
+if gene_name:
+    print(f"The gene name for Entrez ID {entrez_id} is {gene_name}.")
+else:
+    print(f"No gene name found for Entrez ID {entrez_id}.")
+