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