import tkinter as tk
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2Tk
from matplotlib.figure import Figure
import numpy as np

class App:
    def __init__(self, root):
        self.root = root
        fig = Figure(figsize=(5, 5), dpi=100)
        self.ax = fig.add_subplot(111)

        self.canvas = FigureCanvasTkAgg(fig, root)
        self.canvas.get_tk_widget().pack(fill="both", expand=True)

        self.toolbar = NavigationToolbar2Tk(self.canvas, root)

        # Create artists once
        self.scatter = self.ax.scatter([], [])
        self.line, = self.ax.plot([], [])

        root.after(1000, self.update_plot)

    def update_plot(self):
        # New data every update
        xs = np.linspace(0, 10, 100)
        ys = np.sin(xs) + np.random.normal(scale=0.1, size=100)

        # Update artists
        self.scatter.set_offsets(np.column_stack((xs, ys)))
        #self.line.set_data(xs, ys) #Uncomment this to see the expected behaviour

        # Autoscale (not working)
        self.ax.relim()
        self.ax.autoscale_view()

        self.canvas.draw_idle()

        # Keep updating
        self.root.after(1000, self.update_plot)

root = tk.Tk()
App(root)
root.mainloop()