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methods.py

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+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+# ask user to input the file path
+def get_file_path():
+    file_path = input("Please enter the file path: ")
+    return file_path
+
+# read the file
+def read_file(file_path):
+    try:
+        data = pd.read_csv(file_path)
+        return data
+    except FileNotFoundError:
+        print("File not found. Please enter a valid file path.")
+        return None
+    except Exception as e:
+        print("An error occurred. Please try again.")
+        return None
+
+# display the columns of the data
+def display_columns(data):
+    print("The columns in the data are: ")
+    for column in data.columns:
+        print(column)
+
+
+# pick the graph type to plot: volcano plot, MA plot, PCA plot, heatmap
+def pick_graph_type():
+    print("Please pick the graph type you would like to plot: ")
+    print("1. Volcano plot")
+    print("2. MA plot")
+    print("3. PCA plot")
+    print("4. Heatmap")
+    graph_type = input("Enter the number of the graph type you would like to plot: ")
+    return graph_type
+
+# volcano plot
+def volcano_plot(data):
+    x_axis = input("Enter the column name for X axis: ")
+    y_axis = input("Enter the column name for Y axis: ")
+    threshold = float(input("Enter the threshold value: "))
+
+    plt.scatter(x=data[x_axis], y=data[y_axis], s=1, label="Not significant")
+
+    # highlight down- or up- regulated genes
+    down = data[(data[x_axis] <= -threshold) & (data[y_axis] >= threshold)]
+    up = data[(data[x_axis] >= threshold) & (data[y_axis] >= threshold)]
+
+    plt.scatter(x=down[x_axis], y=down[y_axis], s=3, label="Down-regulated", color="blue")
+    plt.scatter(x=up[x_axis], y=up[y_axis], s=3, label="Up-regulated", color="red")
+
+    plt.xlabel(x_axis)
+    plt.ylabel(y_axis)
+    plt.axvline(-threshold, color="grey", linestyle="--")
+    plt.axvline(threshold, color="grey", linestyle="--")
+    plt.axhline(threshold, color="grey", linestyle="--")
+    plt.legend()
+    plt.show()
+
+
+
+# main function
+
+df = pd.read_csv('test.csv')
+volcano_plot(df)