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streamlit_app.py
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streamlit_app.py
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#!/usr/bin/env python3
"""
#####################################################
## ##
## -- STREAMLIT MAIN APP -- ##
## ##
#####################################################
"""
import numpy as np
import pandas as pd
import streamlit as st
from utils.stats_plotting import * # plotting functions
from utils.spectra_plotting import * # spectra view
from utils.filter_dataframes import filter_dataframes # filter files functions
# main page content
def main_page():
title = st.title("Fragment Explorer")
sub_title1 = st.header("About Fragannot and Fragment Explorer")
general_description = \
"""
We created a workflow for exploring internal ions from raw spectra and identified spectra given in various formats. A comprehensive nomenclature for internal ions allows their precise definition and the calculation of their masses. The nomenclature was implemented into a new tool for annotating fragment ions that we titled **"Fragannot"**. This tool outputs fragment annotations as a *.json* or *.csv* files. The *.csv* files can then read with the tool - **"Fragment Explorer"** - to create fragment centric and spectrum centric statistics as well as multiple interactive visualizations.
Fragannot can be downloaded for free from [github.com/arthur-grimaud/fragannot](https://github.com/arthur-grimaud/fragannot).
"""
text_1 = st.markdown(general_description)
# Decripbe project, goal and members
text_2 = st.markdown("We are calculating the mass of the fragments as described in the following:")
# Add forumula for nomenclatur and mass
formula = st.latex(r"""M(fragment)= \frac{M(peptide)+\Delta M(IonCap_{start})-\Delta M(IonCap_{end})+M(H)\times charge -M(formular) } {charge}""")
text_3 = st.markdown("Fragannot results can be analyzed below:")
sub_title2 = st.header("Data Import")
fragments = st.file_uploader("Upload the fragment-centric .csv output of Fragannot:",
type = ["csv"],
help = "Upload the fragment-centric .csv output of Fragannot."
)
spectra = st.file_uploader("Upload the spectrum-centric .csv output of Fragannot:",
type = ["csv"],
help = "Upload a identification file that contains PSMs of the spectrum file in mzID format."
)
text_4 = st.markdown("Fragannot results can be further filtered with the filtering options below (optional).")
with st.expander("Expand filtering options:"):
text_5 = st.markdown("**Select filtering options below:**")
start_seq_length, end_seq_length = st.select_slider("Peptide sequence lenght:",
options = range(0, 5001),
value = (0, 5000),
help = "For 'Spectrum-centric Statistics' only spectra with peptides withing range are considered.")
start_frag_len, end_frag_len = st.select_slider("Fragment ion sequence lenght:",
options = range(0, 1001),
value = (0, 1000),
help = "For 'Fragment-centric Statistics' only fragments within in range are considered.")
start_mz, end_mz = st.select_slider("Select m/z range for internal fragments:",
options = range(0, 100001),
value = (0, 100000),
help = "For 'Fragment-centric Statistics' only fragments within in range are considered.")
start_int, end_int = st.select_slider("Select intensity range for internal fragments:",
options = range(0, 1000001),
value =(0, 1000000),
help = "For 'Fragment-centric Statistics' only fragments within in range are considered.")
data_text = st.markdown("Select which ions to analyse.")
N_ion = st.checkbox("Non-annotated ions", value = True)
check_col1, check_col2 = st.columns(2)
with check_col2:
ions_checkbox_nterm = st.markdown("N-terminal ions")
A_ion = st.checkbox("A ions", value = True)
B_ion = st.checkbox("B ions", value = True)
C_ion = st.checkbox("C ions", value = True)
Cdot_ion = st.checkbox("Cdot ions", value = True)
Cm1_ion = st.checkbox("C-1 ions", value = True)
Cp1_ion = st.checkbox("C+1 ions", value = True)
with check_col1:
ions_checkbox_cterm = st.markdown("C-terminal ions")
X_ion = st.checkbox("X ions", value = True)
Y_ion = st.checkbox("Y ions", value = True)
Z_ion = st.checkbox("Z ions", value = True)
Zdot_ion = st.checkbox("Zdot ions", value = True)
Zp1_ion = st.checkbox("Z+1 ions", value = True)
Zp2_ion = st.checkbox("Z+2 ions", value = True)
Zp3_ion = st.checkbox("Z+3 ions", value = True)
ion_filter_param = [N_ion, A_ion, B_ion, C_ion, Cdot_ion, Cm1_ion, Cp1_ion, X_ion, Y_ion, Z_ion, Zdot_ion, Zp1_ion, Zp2_ion, Zp3_ion]
l1, l2, center_button, r1, r2 = st.columns(5)
with center_button:
run_analysis = st.button("Analyze and filter files!")
if run_analysis and fragments is not None and spectra is not None:
st.session_state["fragments_df"] = pd.read_csv(fragments)
st.session_state["spectra_df"] = pd.read_csv(spectra)
st.session_state["filtered_dfs"] = filter_dataframes([st.session_state["fragments_df"], st.session_state["spectra_df"]],
start_seq_length,
end_seq_length,
start_frag_len,
end_frag_len,
start_mz,
end_mz,
start_int,
end_int,
ion_filter_param)
data_text = st.success("Finished data processing!")
if "filtered_dfs" in st.session_state:
filt_dfs = st.session_state["filtered_dfs"]
st.table(filt_dfs[0].head(10))
sub_title3 = st.header("Fragment-centric Statistics")
plot1_col1, plot2_col2 = st.columns(2)
with plot1_col1:
plot1_title = st.header("Histogram of ion types:")
plot1 = st.plotly_chart(common_type_hist(filt_dfs[0]), use_container_width = True)
with plot2_col2:
plot2_title = st.header("Pie chart of ion types:")
plot2 = st.plotly_chart(common_type_pie(filt_dfs[0]), use_container_width = True)
plot3_title = st.header("Histogram of m/z per ion type:")
plot3 = st.plotly_chart(mz_dist_ion_type(filt_dfs[0]), use_container_width = True)
plot4_col1, plot5_col2 = st.columns(2)
with plot4_col1:
plot4_title = st.header("Log Intensities Distribution:")
plot4 = st.plotly_chart(rel_ion_intens_perc(filt_dfs[0]), use_container_width = True)
with plot5_col2:
# relative intensity to total intensity distribution of different ions
plot5_title = st.header("Relative Log Intensities:")
plot5 = st.plotly_chart(rel_ion_intens_ridge(filt_dfs[0]), use_container_width = True)
sub_title4 = st.header("Spectrum-centric Statistics")
plot6_col1, plot7_col2 = st.columns(2)
with plot6_col1:
plot6_title = st.header("Ion type per spectrum:")
plot6 = st.plotly_chart(per_spec_ion_type(filt_dfs[1]), use_container_width = True)
with plot7_col2:
plot7_title = st.header("Log Intensities")
plot7 = st.plotly_chart(per_spec_ion_intens(filt_dfs[1]), use_container_width = True)
plot8_title = st.header("Logo view of internal fragments:")
plot8_text_1 = st.markdown("Select number of top spectra with the highest number of internal ions to inlcude in logo. Choose 0 for making a logo of all spectra.")
plot8_topn = st.number_input("Choose number of spectra in logo:", min_value = 0, max_value = 3, step = 1)
p8_min_length_logo, p8_max_length_logo = st.select_slider("Peptide sequence lenght:",
options = range(0,21),
value = (0,20))
plot8 = st.pyplot(logo_of_fraction(filt_dfs[1], filt_dfs[0], plot8_topn, p8_max_length_logo, p8_min_length_logo))
# side bar and main page loader
def main():
about_str = \
"""
Fragment Explorer is a small program to explore fragment ions in mass spectra.
"""
st.set_page_config(page_title = "Internal ions",
page_icon = ":test_tube:",
layout = "wide",
initial_sidebar_state = "expanded",
menu_items = {"Get Help": "https://github.com/veitveit/eubic23_internal_ions/discussions",
"Report a bug": "https://github.com/veitveit/eubic23_internal_ions/issues",
"About": about_str}
)
title = st.sidebar.title("Fragment Explorer - EuBIC 2023 Hackathon")
logo = st.sidebar.image("img/logo.png")
doc = st.sidebar.markdown(about_str)
contact_str = "**Contact:** [Arthur Grimaud](mailto:agrimaud@bmb.sdu.dk), [Caroline Lennartsson](mailto:caroline.lennartsson@cpr.ku.dk), [Kristian Boje Nielsen](krisn16@student.sdu.dk), [Louise Buur](louise.buur@fh-hagenberg.at), [Micha Birklbauer](mailto:micha.birklbauer@gmail.com), [Mohieddin Jafari](mohieddin.jafari@helsinki.fi), [Veit Schwämmle](veits@bmb.sdu.dk), [Vladimir Gorshkov](homer2k@gmail.com), [Zoltan Udvardy](zoltan.udvardy.ipbs@gmail.com) "
contact = st.sidebar.markdown(contact_str)
license_str = "**License:** [MIT License](https://github.com/veitveit/eubic23_internal_ions/blob/master/LICENSE.md)"
license = st.sidebar.markdown(license_str)
main_page()
if __name__ == "__main__":
main()