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feat: adding web explore #14

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feat: adding web explore #14

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dfa408d
default import works to LAPIS
Jan 24, 2025
2da9aed
adding mutations over time
Jan 24, 2025
4d2f25c
add steps to the goal
Jan 24, 2025
6a76708
trying to connect to localhost
Jan 24, 2025
bff8476
query for proportions
Jan 24, 2025
05a6640
component working
Jan 27, 2025
c227b34
description and datafilter
Jan 27, 2025
c85071b
only show mutations on request
Jan 27, 2025
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4 changes: 3 additions & 1 deletion app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,15 @@
import variant_deconv
import resistance_mut
import resistance_mut_silo
import web_explorer

PAGES = {
"Home": {"module": index},
"Mutation Frequency": {"module": mutation_freq},
"Variant Deconvolution": {"module": variant_deconv},
"Resistance Mutations (clinical)": {"module": resistance_mut},
"Resistance Mutations (ww)": {"module": resistance_mut_silo}
"Resistance Mutations (ww)": {"module": resistance_mut_silo},
"Web Explore": {"module": web_explorer}
}

def sidebar():
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5 changes: 3 additions & 2 deletions resistance_mut_silo.py
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Expand Up @@ -142,8 +142,9 @@ def app():
# Apply the lambda function to each element in the mutations list
formatted_mutations = [format_mutation(mutation) for mutation in mutations]

st.write(f"Selected mutations:")
st.write(formatted_mutations)
if st.button("Show Mutations"):
st.write(f"Selected mutations:")
st.write(formatted_mutations)


# Allow the user to choose a date range
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59 changes: 59 additions & 0 deletions web_explorer.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,59 @@
import streamlit as st
import streamlit.components.v1 as components
import pandas as pd

LAPIS_URL = "http://localhost:8080"


def app():

## Add a title
st.title("V-Pipe Web Explorer")

## Add a header
st.header("Explore Mutations Over Time")

## Add a subheader
st.subheader("This page allows you to explore mutations over time by gene and proportion.")

## select dat range
st.write("Select a date range:")
date_range = st.date_input("Select a date range:", [pd.to_datetime("2024-09-30"), pd.to_datetime("2024-10-16")])

## Add a horizontal line
st.markdown("---")

start_date = date_range[0].strftime("%Y-%m-%d")
end_date = date_range[1].strftime("%Y-%m-%d")

components.html(
f"""
<html>
<head>
<script type="module" src="https://unpkg.com/@genspectrum/dashboard-components@latest/standalone-bundle/dashboard-components.js"></script>
<link rel="stylesheet" href="https://unpkg.com/@genspectrum/dashboard-components@latest/dist/style.css" />
</head>
<body>
<!-- Component documentation: https://genspectrum.github.io/dashboard-components/?path=/docs/visualization-mutations-over-time--docs -->
<gs-app lapis="{LAPIS_URL}">
<gs-mutations-over-time
lapisFilter='{{"sampling_dateFrom":"{start_date}", "sampling_dateTo": "{end_date}"}}'
sequenceType='amino acid'
views='["grid"]'
width='100%'
height='100%'
granularity='day'
lapisDateField='sampling_date'
/>
</gs-app>
</head>
<body>
</body>
</html>
""",
height=3000,
)


if __name__ == "__main__":
app()