This is the default behaviour of scatter plots in matplotlib:
x = [1, 2, 3]
y = [10, 20, 40]
plt.scatter(x, y)
To make the axes start with the minimum value and end in the maximum value. You can use plt.xlim() and plt.ylim() like this:
x = [1, 2, 3]
y = [10, 20, 40]
plt.xlim(min(x), max(x))
plt.ylim(min(y), max(y))
plt.scatter(x, y)
You will notice that the values are still there, but it’s barely visible. This is why the default behaviour of scatter plots is to set the axes larger than the value range.