script for DR curves and first steps for tool development

tools/tox_tools/dose_responses/dose_response.py

@@ -0,0 +1,37 @@
+import argparse
+import pandas as pd
+from py50.calculator import Calculator
+from py50.plotcurve import PlotCurve
+import matplotlib.pyplot as plt
+
+
+parser = argparse.ArgumentParser(description="Calculate IC50 values, plot dose-response curves, and save results.")
+parser.add_argument('file_path', type=str, help='Path to the CSV file containing the data.')
+parser.add_argument('--plot_title', type=str, default='Default Plot Single Example (Positive)', help='Title for the plot.')
+parser.add_argument('--drug_name', type=str, default='Drug 1', help='Name of the drug for labeling purposes.')
+parser.add_argument('--output_plot', type=str, default='dose_response_curve.jpg', help='File name for saving the output plot as JPG.')
+parser.add_argument('--output_ic50', type=str, default='ic50_values.txt', help='File name for saving the IC50 values as a text file.')
+args = parser.parse_args()
+
+
+df = pd.read_csv(args.file_path)
+
+data = Calculator(df)
+ic50 = data.calculate_ic50(name_col='compound', concentration_col='concentration', response_col='effect')
+
+with open(args.output_ic50, 'w') as f:
+    f.write(f"IC50 Value: {ic50}\n")
+
+plot_data = PlotCurve(df)
+fig, ax = plt.subplots()
+fig = plot_data.single_curve_plot(ax=ax,
+                            concentration_col='concentration',
+                            response_col='effect',
+                            plot_title=args.plot_title,
+                            drug_name=args.drug_name,
+                            xlabel='Concentration',
+                            ylabel='Effect',
+                            legend=True)
+
+fig.savefig(args.output_plot, format='jpg', dpi=300)
+

tools/tox_tools/dose_responses/test-data/single_example.csv

@@ -0,0 +1,11 @@
+compound,concentration,effect,% Inhibition 2,% Inhibition Avg
+Drug 1,100000,90,94,92
+Drug 1,33300,97,89,93
+Drug 1,11100,86,89,88
+Drug 1,3700,81,88,84
+Drug 1,1240,63,70,67
+Drug 1,412,36,47,41
+Drug 1,137,22,11,16
+Drug 1,45.7,-4,-3,-3
+Drug 1,15.2,11,-3,4
+Drug 1,5,-14,-11,-12