kegg highlight additional compounds

routes/apps/_kegg.py

@@ -14,7 +14,6 @@
 from Bio.KEGG.KGML import KGML_parser
 from Bio.Graphics.KGML_vis import KGMLCanvas
 from Bio.Graphics.ColorSpiral import ColorSpiral
-#from IPython.display import Image, HTML
 import tempfile
 
 
@@ -62,10 +61,23 @@ def organism_options(cache, pathway_id):
 
     return [{'label': org, 'value': org} for org in org_value.split(',')]
 
+def additional_compound_options(cache, pathway_id, organism_id):
+    compound_pathway_data=read_compound_pathway(cache)
+    try:
+        pathname = pathway_id.replace("map", organism_id)    
+        pathway=KGML_parser.read(kegg_get(pathname, "kgml"))
+        compound_list=[]
+        for compound in pathway.compounds :
+            c=compound.name.split(":")[-1]
+            compound_list.append(c)
 
+        # return [{'label': id, 'value': id} for id in compound_list] if compound_list else []
+        return [{'label': f"{id}: {compound_pathway_data.loc[compound_pathway_data['compound_id'] == id, 'compound_name'].values[0]}" 
+            if not compound_pathway_data.loc[compound_pathway_data['compound_id'] == id, 'compound_name'].empty else id, 'value': id} for id in compound_list] if compound_list else []
+    except:
+        return []
 
-
-def network_pdf(selected_compound, pathway_id, organism_id):
+def network_pdf(selected_compound, pathway_id, organism_id, additional_compound):
     # Clean up previous kegg files, clean all if total pdfs more than 50, else clean 30 mins or older files
     kegg_files = glob.glob("/tmp/kegg-*.pdf")
     if len(kegg_files) > 20:
@@ -80,6 +92,8 @@ def network_pdf(selected_compound, pathway_id, organism_id):
 
         for compound in pathway.compounds :
             c=compound.name.split(":")[-1]
+            if c in additional_compound:
+                compound.graphics[0].bgcolor="#FFFF00"
             if c in selected_compound:
                 compound.graphics[0].bgcolor="#FF0000"
 

routes/apps/kegg.py

@@ -27,7 +27,7 @@
 import plotly.express as px
 # from plotly.io import write_image
 import plotly.graph_objects as go
-from ._kegg import compound_options, pathway_options, organism_options, network_pdf
+from ._kegg import compound_options, pathway_options, organism_options, additional_compound_options, network_pdf
 from dash import dash_table
 
 import io
@@ -124,7 +124,8 @@ def make_loading(children,i):
                                     html.H5("Filters", style={"margin-top":10}), 
                                     html.Label('Compound'), make_loading( dcc.Dropdown( id='opt-compound', multi=True, optionHeight=120), 1),
                                     html.Label('Pathway',style={"margin-top":10}),  make_loading( dcc.Dropdown( id='opt-pathway', optionHeight=90), 2 ),
-                                    html.Label('Organism',style={"margin-top":10}),  make_loading( dcc.Dropdown( id='opt-organism', placeholder="No Pathway Selected"), 3 ),
+                                    html.Label('Organism',style={"margin-top":10}),  make_loading( dcc.Dropdown( id='opt-organism'), 3 ),
+                                    html.Label('Highlight Additional Compound',style={"margin-top":10}),  make_loading( dcc.Dropdown( id='opt-additional', multi=True, optionHeight=120), 4 ),
                                     html.Label('Download file prefix',style={"margin-top":10}), 
                                     dcc.Input(id='download_name', value="kegg", type='text',style={"width":"100%", "height":"34px"})
                                 ],
@@ -203,6 +204,18 @@ def update_organisms(selected_pathway):
         return [], "No Organism Found for Selected Pathway" 
     return org_options, "Select Organism"
 
+# Callback to update opt-additional based on selected pathway and organism
+@dashapp.callback(
+    Output('opt-additional', 'options'),
+    Output('opt-additional', 'placeholder'),
+    Input('opt-pathway', 'value'),
+    Input('opt-organism', 'value')
+)
+def update_additional(selected_pathway, selected_organism):
+    if selected_pathway is None or selected_organism is None:
+        return [], "No Available Compound"
+    return additional_compound_options(cache, selected_pathway, selected_organism), "Select Additional Compound"
+
 
 # Callback on submit
 @dashapp.callback(
@@ -212,16 +225,17 @@ def update_organisms(selected_pathway):
     State("opt-compound", "value"),
     State("opt-pathway", "value"),
     State("opt-organism", "value"),
+    State("opt-additional", "value"),
     State('download_name','value'),
 )
-def update_output(session_id, n_clicks, compound, pathway, organism, download_name):
+def update_output(session_id, n_clicks, compound, pathway, organism, additional_compound, download_name):
     if not n_clicks:
         return html.Div([])
 
     if not compound or pathway is None or organism is None:
         return html.Div([dcc.Markdown("*** Please select at least a compound, pathway and organism!", style={"margin-top":"15px","margin-left":"15px"})])
 
-    pdf_path=network_pdf(compound,pathway,organism)
+    pdf_path=network_pdf(compound, pathway, organism, additional_compound)
     if pdf_path is None:
         return html.Div([dcc.Markdown("*** Failed to generate network pdf!", style={"margin-top":"15px","margin-left":"15px"})])