diff --git a/analysis/Python_scripts/add_zeros.ipynb b/analysis/Python_scripts/add_zeros.ipynb
index d7d05ee..09a0b49 100644
--- a/analysis/Python_scripts/add_zeros.ipynb
+++ b/analysis/Python_scripts/add_zeros.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 25,
"metadata": {},
"outputs": [],
"source": [
@@ -10,37 +10,32 @@
"from matchms.importing import load_from_msp\n",
"from matchms.logging_functions import set_matchms_logger_level\n",
"import itertools\n",
+ "from utils import load_spectra_metadata\n",
"\n",
"set_matchms_logger_level(\"ERROR\")"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 26,
"metadata": {},
"outputs": [],
"source": [
- "predicted_spectra = list(load_from_msp(\"../data/filtered/simulated_matchms_filter_1%I_all_peaks.msp\"))\n",
- "predicted_spectra_metadata= pd.DataFrame.from_dict([x.metadata for x in predicted_spectra])\n",
- "predicted_spectra_metadata.rename(columns={'compound_name': 'query'}, inplace=True)\n",
- "predicted_spectra_names = predicted_spectra_metadata['query'].to_list()"
+ "predicted_spectra, predicted_spectra_metadata, predicted_spectra_names = load_spectra_metadata(\"../data/filtered/simulated_matchms_filter_1%I_all_peaks.msp\", 'query')"
]
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 27,
"metadata": {},
"outputs": [],
"source": [
- "experimental_spectra = list(load_from_msp(\"../data/experimental/RECETOX_GC-EI_MS_20201028.msp\"))\n",
- "experimental_spectra_metadata= pd.DataFrame.from_dict([x.metadata for x in experimental_spectra])\n",
- "experimental_spectra_metadata.rename(columns={'compound_name': 'reference'}, inplace=True)\n",
- "experimental_spectra_names = experimental_spectra_metadata['reference'].to_list()"
+ "experimental_spectra, experimental_spectra_metadata, experimental_spectra_names = load_spectra_metadata(\"../data/experimental/RECETOX_GC-EI_MS_20201028.msp\", 'reference')"
]
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
@@ -49,7 +44,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
@@ -59,7 +54,7 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 30,
"metadata": {},
"outputs": [],
"source": [
@@ -69,7 +64,7 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": 31,
"metadata": {},
"outputs": [],
"source": [
@@ -79,7 +74,7 @@
},
{
"cell_type": "code",
- "execution_count": 16,
+ "execution_count": 32,
"metadata": {},
"outputs": [],
"source": [
diff --git a/analysis/Python_scripts/scatterplot.ipynb b/analysis/Python_scripts/scatterplot.ipynb
index f2cbe54..4ab3414 100644
--- a/analysis/Python_scripts/scatterplot.ipynb
+++ b/analysis/Python_scripts/scatterplot.ipynb
@@ -2,46 +2,37 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
- "import numpy as np\n",
"import plotly.graph_objs as go\n",
"import pandas as pd\n",
- "from rdkit import Chem\n",
"from matchms.importing import load_from_msp\n",
"from matchms.logging_functions import set_matchms_logger_level\n",
"\n",
- "from utils import is_spectrum_for_compound\n",
+ "from utils import is_spectrum_for_compound, load_spectra_metadata\n",
"\n",
"set_matchms_logger_level('ERROR')"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"matchms_scores = pd.read_csv(\"../data/output_matching/matchms/matchms_tol_0.01_1%I_all_peaks_with_0s.tsv\", sep=\"\\t\")\n",
- "\n",
"matchms_scores = matchms_scores[matchms_scores.apply(lambda x: is_spectrum_for_compound(x['query'], x['reference']), axis=1)]\n",
"\n",
- "molecules = Chem.SDMolSupplier(\"../../data/RECETOX_GC-EI-MS_20201028.sdf\")\n",
- "\n",
- "predicted_spectra = list(load_from_msp(\"../data/filtered/simulated_matchms_filter_1%I_all_peaks.msp\"))\n",
- "spectra_metadata = pd.DataFrame.from_dict([x.metadata for x in predicted_spectra])\n",
- "spectra_metadata.rename(columns={'compound_name': 'query'}, inplace=True)\n",
+ "_ , spectra_metadata, _ = load_spectra_metadata(\"../data/filtered/simulated_matchms_filter_1%I_all_peaks.msp\", 'query')\n",
"\n",
- "reference_spectra = list(load_from_msp(\"../data/experimental/RECETOX_GC-EI_MS_20201028.msp\"))\n",
- "reference_spectra_metadata = pd.DataFrame.from_dict([x.metadata for x in reference_spectra])\n",
- "reference_spectra_metadata.rename(columns={'compound_name': 'reference'}, inplace=True)\n"
+ "_ , reference_spectra_metadata, _ = load_spectra_metadata(\"../data/experimental/RECETOX_GC-EI_MS_20201028.msp\", 'reference')"
]
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
@@ -54,13 +45,12 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
- "merged['CosineHungarian_0.01_0.0_1.0_matches'] = pd.to_numeric(merged['CosineHungarian_0.01_0.0_1.0_matches'], errors='coerce')\n",
- "merged['n_peaks_query'] = pd.to_numeric(merged['n_peaks_query'], errors='coerce')\n",
- "merged['n_peaks_reference'] = pd.to_numeric(merged['n_peaks_reference'], errors='coerce')\n",
+ "numeric_columns = ['CosineHungarian_0.01_0.0_1.0_matches', 'n_peaks_query', 'n_peaks_reference']\n",
+ "merged[numeric_columns] = merged[numeric_columns].apply(pd.to_numeric, errors='coerce')\n",
"\n",
"merged['FractionQuery'] = merged['CosineHungarian_0.01_0.0_1.0_matches'] / merged['n_peaks_query']\n",
"merged['FractionReference'] = merged['CosineHungarian_0.01_0.0_1.0_matches'] / merged['n_peaks_reference']"
@@ -68,9 +58,38 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 5,
"metadata": {},
"outputs": [
+ {
+ "data": {
+ "text/html": [
+ " \n",
+ " "
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
{
"data": {
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