Update app.py

app.py

@@ -11,6 +11,7 @@ LLR_FILE='ALL_hum_isoforms_ESM1b_LLR.zip'
 
 df=pd.read_csv('isoform_list.csv',index_col=0)
 uids=list(df.index.values)
+clinvar = pd.read_csv('clinvar.csv.gz')
 
 def load_LLR(uniprot_id):
   '''Loads the LLRs for a given uniprot id. Returns a 20xL dataframe 
@@ -23,7 +24,7 @@ def load_LLR(uniprot_id):
   return pd.read_csv(data,index_col=0)
 
 
-def plot_interactive(uniprot_id):
+def plot_interactive(uniprot_id, show_clinvar=False):
   primaryLLR = load_LLR(uniprot_id)
   
   template='plotly_white'
@@ -46,6 +47,30 @@ def plot_interactive(uniprot_id):
           " (%{z:.2f})", 
       ])+'<extra></extra>'
   )
+  if show_clinvar:
+    iso_clinvar = clinvar[clinvar.LLR_file_id == uniprot_id]
+    hwt_x=[]
+    hwt_y=[]
+    cust=[]
+    for i in primaryLLR.columns:
+      for j in list(primaryLLR.index):
+        mut = i[0]+i[2:]+j
+        if mut in iso_clinvar.variant:
+                        hwt_x+=[i]
+                        hwt_y+=[j]
+                        cust+=[primaryLLR.loc[j,i]]
+
+    fig.add_trace(go.Scatter(
+        x=hwt_x,
+        y=hwt_y,
+        customdata=cust,
+        mode='markers',
+        marker=dict(size=8),
+        hovertemplate="<br>".join([
+            "<b>%{x} %{y}</b>"+
+            " (%{customdata:.2f})", 
+        ])+'<extra></extra>')
+    )
   
   return fig
   
@@ -53,6 +78,8 @@ def plot_interactive(uniprot_id):
 selection = st.selectbox("uniprot_id:", df)
 uid=df[df.txt==selection].index.values[0]
 
-fig = plot_interactive(uid)
+show_clinvar = st.checkbox('show clinvar annotations')
+
+fig = plot_interactive(uid,show_clinvar=show_clinvar)
 fig.update_layout(width = 800, height = 600, autosize = False)
 st.plotly_chart(fig, use_container_width=True)