plot MS2 spectrum

streamlit_app/FAIR_MS_Library_Editor.py

@@ -65,3 +65,6 @@
                 #     st.write(datasets_metadata[key].keys())
             # st.write(datasets[dataset_key])
         # st.json(datasets)
+
+    if 'spectra' in st.session_state:
+        spectra = st.session_state["spectra"]

streamlit_app/pages/1_File_Import.py

@@ -63,6 +63,7 @@ def extract_metadata(df, keys):
     st.write(df_spectra)
 
 
+    st.session_state['spectra'] = spectra
     st.session_state['df_spectra'] = df_spectra
     st.session_state['len_spectra'] = len(df_spectra)
 

streamlit_app/pages/2_Plot_spectrum.py

@@ -0,0 +1,58 @@
+from matchms.plotting.spectrum_plots import plot_spectra_mirror, plot_spectrum
+import streamlit as st
+import matplotlib.pyplot as plt
+import pandas as pd
+import numpy as np
+import pubchempy
+from rdkit import Chem
+from rdkit.Chem import Draw
+
+
+
+
+st.set_page_config(
+    layout="wide", 
+    page_title="Library Export - FAIR MS Library Curation Editor", 
+    #page_icon="assets/favicon.ico",
+    menu_items={
+        'Get Help': 'https://github.com/mzmine/biohack23_p15',
+        'Report a bug': "https://github.com/mzmine/biohack23_p15/issues/new/choose",
+        'About': "# This is the creation and curation wizard for FAIR MS Libraries."
+    }
+)
+
+
+st.markdown("## Plot selected MS2 spectrum")
+st.markdown("Please select a spectrum based on compound_name")
+
+
+spectra = st.session_state['spectra'] 
+df_spectra = st.session_state['df_spectra']
+
+cmp_list = df_spectra["compound_name"].tolist()
+
+st.markdown("## Select a compound name")
+cmp_selector = st.selectbox(
+    "select a compound name",
+    cmp_list
+)
+
+if cmp_selector in cmp_list:
+    cmp_id = cmp_list.index(cmp_selector)
+    cmp_smile = df_spectra.loc[cmp_id]["smiles"]
+
+
+    plt_spectrum = spectra[cmp_id]
+
+    fig, axs = plt.subplots(1, 2, figsize=(12.8, 4.2), gridspec_kw={'width_ratios': [2, 5]}, sharey=False)
+    cmp_img = Chem.Draw.MolToImage(Chem.MolFromSmiles(cmp_smile), ax=axs[0])
+
+    axs[0].grid(False)
+    axs[0].tick_params(axis='both', bottom=False, labelbottom=False, left=False, labelleft=False)
+    axs[0].set_title(cmp_smile)
+    axs[0].imshow(cmp_img)
+    axs[0].axis("off")
+
+    plot_spectrum(plt_spectrum, axs[1])
+
+    st.pyplot(fig)