add query params support and gene_symbol

app.py

@@ -6,6 +6,21 @@ import altair as alt
 
 st.set_page_config(layout='wide')
 
+# parse out gene_ids from URL query args to it's possible to link to this page
+query_params = st.query_params()
+if "gene_id_1" %in% names(query_params):
+    gene_id_1 = query_params["gene_id_1"]
+else:
+    gene_id_1 = "CNAG_04365"
+
+if "gene_id_2" %in% names(query_params):
+    gene_id_2 = query_params["gene_id_2"]
+else:
+    gene_id_2 = "CNAG_04222"
+
+    
+
+
 st.markdown("""
 # CryptoCEN Expression Scatter
 **CryptoCEN** is a co-expression network for *Cryptococcus neoformans* built on 1,524 RNA-seq runs across 34 studies.
@@ -45,26 +60,28 @@ col1, col2, padding = st.columns(spec = [0.2, 0.2, 0.6])
 with col1:
     gene_id_1 = st.text_input(
         label = "Gene ID 1",
-        value = "CNAG_04365",
+        value = f"{gene_id_1}",
         max_chars = 10,
         help = "CNAG Gene ID e.g. CNAG_04365")
 
 with col2:
     gene_id_2 = st.text_input(
         label = "Gene ID 2",
-        value = "CNAG_04222",
+        value = f"{gene_id_2}",
         max_chars = 10,
         help = "CNAG Gene ID e.g. CNAG_04222")
 
 # check the user input
 try:
-    cnag_id_1 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_1]["cnag_id"].values
+    cnag_id_1 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_1]["cnag_id"].values[0]
+    gene_symbol_1 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_1]["gene_symbol"].values[0]
     description_1 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_1]["description"].values[0]
 except:
     st.error(f"Unable to locate cnag_id for Gene ID 1: {gene_id_1}, it should be of the form 'CNAG_######'")
 
 try:
-    cnag_id_2 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_2]["cnag_id"].values
+    cnag_id_2 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_2]["cnag_id"].values[0]
+    gene_symbol_2 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_2]["gene_symbol"].values[0]
     description_2 = h99_transcript_annotations.loc[h99_transcript_annotations["gene_id"] == gene_id_2]["description"].values[0]
 except:
     st.error(f"Unable to locate cnag_id for Gene ID 2: {gene_id_2}, it should be of the form 'CNAG_######'")
@@ -79,12 +96,14 @@ chart_data = chart_data.merge(
 
 st.markdown(f"""
 #### Gene 1:
-* *gene_id*: [{gene_id_1}](https://fungidb.org/fungidb/app/record/gene/{gene_id_1})
-* *description*: {description_1}
+* *Gene ID*: [{gene_id_1}](https://fungidb.org/fungidb/app/record/gene/{gene_id_1})
+{'* *Gene Symbol*:' + gene_symbol_1 if gene_symbol_1 is not None else ''}
+* *Description*: {description_1}
 
 #### Gene 2:
-* *gene_id*: [{gene_id_2}](https://fungidb.org/fungidb/app/record/gene/{gene_id_2})
-* *description*: {description_2}
+* *Gene ID*: [{gene_id_2}](https://fungidb.org/fungidb/app/record/gene/{gene_id_2})
+{'* *Gene Symbol*:' + gene_symbol_2 if gene_symbol_2 is not None else ''}
+* *Description*: {description_2}
 """)
 
 chart = (