app.py

import streamlit as st
st.set_page_config(layout="wide")
import pandas as pd
import numpy as np
from zipfile import ZipFile

import plotly.express as px
import plotly.graph_objs as go

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 
     rows are indexed by AA change, 
     (AAorder=['K','R','H','E','D','N','Q','T','S','C','G','A','V','L','I','M','P','Y','F','W'])
     columns indexed by WT_AA+position e.g, "G 12"
     Usage example: load_LLR('P01116') or load_LLR('P01116-2')'''
  with ZipFile(LLR_FILE) as myzip:
    data = myzip.open(myzip.namelist()[0]+uniprot_id+'_LLR.csv')
  return pd.read_csv(data,index_col=0)
  
def meltLLR(LLR,gene_prefix=None,ignore_pos=False):
  vars = LLR.melt(ignore_index=False)
  vars['variant'] = [''.join(i.split(' '))+j for i,j in zip(vars['variable'],vars.index)]
  vars['score'] = vars['value']
  vars = vars.set_index('variant')
  if not ignore_pos:
    vars['pos'] = [int(i[1:-1]) for i in vars.index]
  del vars['variable'],vars['value']
  if gene_prefix is not None:
    vars.index=gene_prefix+'_'+vars.index
  return vars

def plot_interactive(uniprot_id, show_clinvar=False):
  primaryLLR = load_LLR(uniprot_id)
  
  template='plotly_white'

  fig = px.imshow(primaryLLR.values, x=primaryLLR.columns, y=primaryLLR.index, color_continuous_scale='Viridis_r',zmax=0,zmin=-20,
                  labels=dict(y="Amino acid change", x="Protein sequence", color="LLR"),
                  template=template,
                  title=selection)
  fig.update_xaxes(tickangle=-90,range=[0,99],rangeslider=dict(visible=True),dtick=1)
  fig.update_yaxes(dtick=1)
  fig.update_layout({
  'plot_bgcolor': 'rgba(0, 0, 0, 0)',
  'paper_bgcolor': 'rgba(0, 0, 0, 0)',
  },font={'family':'Arial','size':11},
  hoverlabel=dict(font=dict(family='Arial', size=14)))

  fig.update_traces(
      hovertemplate="<br>".join([
          "<b>%{x} %{y}</b>"+
          " (%{z:.2f})", 
      ])+'<extra></extra>'
  )
  if show_clinvar:
    iso_clinvar = clinvar[clinvar.LLR_file_id == uniprot_id]
    iso_clinvar = iso_clinvar[iso_clinvar.ClinicalSignificance.isin(['Benign','Pathogenic'])]
    b_mut=set(iso_clinvar[iso_clinvar.ClinicalSignificance=='Benign'].variant.values)
    p_mut=set(iso_clinvar[iso_clinvar.ClinicalSignificance=='Pathogenic'].variant.values)
    hwt_x=[]
    hwt_y=[]
    cust=[]
    phwt_x=[]
    phwt_y=[]
    pcust=[]
    for i in primaryLLR.columns:
      for j in list(primaryLLR.index):
        mut = i[0]+i[2:]+j
        if mut in b_mut:
                        hwt_x+=[i]
                        hwt_y+=[j]
                        cust+=[primaryLLR.loc[j,i]]
        elif mut in p_mut:
                        phwt_x+=[i]
                        phwt_y+=[j]
                        pcust+=[primaryLLR.loc[j,i]]

    fig.add_trace(go.Scatter(
        x=phwt_x,
        y=phwt_y,
        customdata=pcust,
        mode='markers',
        marker=dict(size=8),
        showlegend=False,
        hovertemplate="<br>".join([
            "<b>%{x} %{y}</b>"+
            " (%{customdata:.2f})", 
        ])+'<extra></extra>')
    )
    fig.add_trace(go.Scatter(
        x=hwt_x,
        y=hwt_y,
        customdata=cust,
        mode='markers',
        showlegend=False,
        marker=dict(size=8),
        hovertemplate="<br>".join([
            "<b>%{x} %{y}</b>"+
            " (%{customdata:.2f})", 
        ])+'<extra></extra>')
    )
  
  return fig
  

selection = st.selectbox("uniprot_id:", df, index= 6251)
uid=df[df.txt==selection].index.values[0]

show_clinvar = st.checkbox('show ClinVar annotations (red: pathogenic, green: benign)',value=False)

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)

st.download_button(
     label="Download data as CSV",
     data=meltLLR(load_LLR(uid)).to_csv(),
     file_name=selection+'.csv',
     mime='text/csv',
 )

st.markdown("""
To obtain ESM effect scores for non-missense mutations (e.g. indels) or non-human proteins, 
please use the [esm-variants command-line tool](https://github.com/ntranoslab/esm-variants).
""")